Input: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xcr Working: n-9-36.cluster.ucsf.bkslab.org:/scratch/xiaobo/167320/xcr-8058097.70 Result: /scratch/xiaobo/167320/xcr-8058097.70 Output: /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcr Task: /mnt/nfs/soft/dock/versions/dock37/DOCK-3.7.4rc1/ligand/generate/build_database_ligand.sh --no-db --no-solv --no-mol2 --single --covalent --pre-tautomerized --permissive-taut-prot /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/inputs/xcr mkdir: created directory `/scratch/xiaobo/167320' mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70' /scratch/xiaobo/167320/xcr-8058097.70 /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs NOTICE: Using permissive tautomer and protomer thresholds. Could produce many protomers! STORE_PROTOMERS is not set! Will keep all results to finished directory mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working' mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/protonate' Storing results in /scratch/xiaobo/167320/xcr-8058097.70/finished Working in /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 /scratch/xiaobo/167320/xcr-8058097.70/working/protonate /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Using inputs as protomers/tautomers. No processing done 477 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/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Bulk generating 3D conformations all protomers in /scratch/xiaobo/167320/xcr-8058097.70/working/3D mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/3D' We are using corina for 3D embeding debuging info:: /scratch/xiaobo/167320/xcr-8058097.70/working/protonate/xcr-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 ZINC001576447066 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building' mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576447066 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 1) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/1 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/1' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576447066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447066 none C[C@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 49, 30, 30, 10, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 49, 50, 50, 50, 50, 49, 49, 49, 30, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 44, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 2) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/2 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/2' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576447066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447066 none C[C@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 44, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576447066 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/finished' Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 Building ZINC001576447066 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576447066 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 1) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576447066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447066 none C[C@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 49, 30, 30, 10, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 49, 50, 50, 50, 50, 49, 49, 49, 30, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 44, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 2) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576447066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447066 none C[C@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 9, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50, 32, 9, 9, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 44, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576447066 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447066 Building ZINC001576447067 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576447067 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 3) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/3 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/3' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576447067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447067 none C[C@@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 31, 31, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 31, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 4) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/4 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/4' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576447067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447067 none C[C@@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 32, 32, 10, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 49, 50, 50, 50, 50, 49, 49, 49, 32, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 44, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576447067 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 Building ZINC001576447067 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576447067 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 3) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/3: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576447067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447067 none C[C@@H](C(=O)NCC1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 31, 31, 11, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 50, 50, 50, 31, 11, 11, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 4) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/4: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1) `ZINC001576447067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576447067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001576447067 none C[C@@H](C(=O)NCC1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 32, 32, 10, 2, 2, 2, 2, 1, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 49, 50, 50, 50, 50, 49, 49, 49, 32, 10, 10, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 10, 11, 44, 13, 14, 15, 16, 17, 18, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576447067 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576447067 Building ZINC001576449340 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576449340 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 5) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/5 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/5' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)CC1) `ZINC001576449340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576449340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576449340 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 31, 31, 31, 31, 34, 34, 35, 36, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 31, 31, 31, 31, 31, 35, 35, 36, 36, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 6) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/6 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/6' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)CC1) `ZINC001576449340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576449340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576449340 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 33, 33, 34, 34, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 31, 31, 31, 31, 31, 34, 34, 34, 34, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576449340 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 Building ZINC001576449340 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576449340 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 5) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)CC1) `ZINC001576449340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576449340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576449340 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 31, 31, 31, 31, 34, 34, 35, 36, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 31, 31, 31, 31, 31, 35, 35, 36, 36, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 6) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)CC1) `ZINC001576449340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576449340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576449340 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCC1CCN(C(=O)CCn2ccnn2)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', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 8, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 31, 31, 31, 31, 33, 33, 34, 34, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 31, 31, 31, 31, 31, 34, 34, 34, 34, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 131 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576449340 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449340 Building ZINC001576449636 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576449636 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 7) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/7 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/7' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001576449636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576449636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576449636 none Cn1cnc(C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 18, 31, 18, 18, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 8) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/8 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/8' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001576449636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576449636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576449636 none Cn1cnc(C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 20, 39, 20, 20, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576449636 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 Building ZINC001576449636 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576449636 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 7) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/7: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001576449636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576449636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576449636 none Cn1cnc(C(=O)N2CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 31, 18, 31, 18, 18, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 18, 50, 50, 50, 50, 50, 18, 18, 18, 18, 18, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18, 18, 18] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 8) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/8: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cnc(C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1) `ZINC001576449636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576449636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576449636 none Cn1cnc(C(=O)N2CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 39, 20, 39, 20, 20, 20, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 20, 50, 50, 50, 50, 50, 20, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 20, 20] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48]) total number of confs: 142 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576449636 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576449636 Building ZINC001576459494 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576459494 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 9) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/9 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/9' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576459494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459494 none C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 42, 45, 45, 49, 50, 50, 33, 42, 33, 33, 33, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 45, 45, 45, 49, 49, 50, 50, 33, 33, 33, 33, 33, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 10) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/10 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/10' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576459494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459494 none C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 40, 44, 44, 48, 50, 50, 34, 40, 34, 34, 34, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 44, 44, 44, 48, 48, 50, 50, 34, 34, 34, 34, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576459494 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 Building ZINC001576459494 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576459494 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 9) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576459494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459494 none C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 42, 45, 45, 49, 50, 50, 33, 42, 33, 33, 33, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 45, 45, 45, 49, 49, 50, 50, 33, 33, 33, 33, 33, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 171 number of broken/clashed sets: 38 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 10) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576459494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459494 none C[C@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [44, 40, 44, 44, 48, 50, 50, 34, 40, 34, 34, 34, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 44, 44, 44, 48, 48, 50, 50, 34, 34, 34, 34, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576459494 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459494 Building ZINC001576459495 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576459495 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 11) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/11 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/11' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576459495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459495 none C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 40, 47, 47, 50, 50, 50, 31, 40, 31, 31, 31, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 47, 47, 47, 50, 50, 50, 50, 31, 31, 31, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 12) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/12 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/12' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576459495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459495 none C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 47, 47, 50, 50, 50, 30, 43, 30, 30, 30, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 47, 47, 47, 50, 50, 50, 50, 30, 30, 30, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576459495 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 Building ZINC001576459495 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576459495 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 11) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576459495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459495 none C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 40, 47, 47, 50, 50, 50, 31, 40, 31, 31, 31, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 47, 47, 47, 50, 50, 50, 50, 31, 31, 31, 31, 31, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 176 number of broken/clashed sets: 39 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 12) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576459495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576459495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576459495 none C[C@@H](CC(N)=O)C(=O)N1CCC(CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 6, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 43, 47, 47, 50, 50, 50, 30, 43, 30, 30, 30, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 47, 47, 47, 50, 50, 50, 50, 30, 30, 30, 30, 30, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 34 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576459495 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576459495 Building ZINC001576517013 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576517013 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 13) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/13 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/13' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1) `ZINC001576517013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576517013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001576517013 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 6, 8, 1, 8, 1, 1, 8, 8, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 14) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/14 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/14' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1) `ZINC001576517013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576517013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001576517013 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 6, 8, 1, 8, 1, 1, 8, 8, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576517013 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 Building ZINC001576517013 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576517013 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 13) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1) `ZINC001576517013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576517013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001576517013 none CCC(C)(C)[C@@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 6, 8, 1, 8, 1, 1, 8, 8, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 14) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1) `ZINC001576517013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576517013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 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: ZINC001576517013 none CCC(C)(C)[C@]([O-])([SiH3])C(=O)N(C)CCCc1[nH]nc(N)c1c1nn[nH]n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 5, 1, 8, 6, 8, 1, 8, 1, 1, 8, 8, 8, 6, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6] dock color type numbers: [7, 7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 1, 3, 3, 1, 1, 1, 1, 1, 1, 1, 4, 8, 8, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 4, 4, 8, 8, 8, 8, 18, 18] 50 rigid atoms, others: [2, 5, 6, 7, 8, 9, 10, 11, 40, 39, 38] set([0, 1, 3, 4, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 61 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576517013 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576517013 Building ZINC001576535828 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576535828 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 15) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/15 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/15' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001576535828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576535828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576535828 none CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 25, 15, 25, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 38, 50, 50, 50, 38, 38, 38, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 38, 38] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 16) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/16 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/16' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001576535828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576535828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576535828 none CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 42, 42, 32, 20, 32, 20, 20, 20, 20, 5, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 42, 50, 50, 50, 42, 42, 42, 20, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576535828 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 Building ZINC001576535828 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576535828 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 15) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001576535828.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576535828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576535828 none CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 50, 38, 38, 25, 15, 25, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 38, 50, 50, 50, 38, 38, 38, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 38, 38] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 170 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 16) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1) `ZINC001576535828.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576535828.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576535828 none CC(=O)N1CC(C(=O)N2CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 42, 42, 32, 20, 32, 20, 20, 20, 20, 5, 20, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 42, 50, 50, 50, 42, 42, 42, 20, 20, 20, 20, 20, 20, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20, 42, 42] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 154 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576535828 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576535828 Building ZINC001576546714 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576546714 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 17) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/17 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/17' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1) `ZINC001576546714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576546714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001576546714 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 45, 45, 45, 50, 50, 45, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 17, 17, 45, 50, 50, 45, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 18) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/18 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/18' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1) `ZINC001576546714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576546714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001576546714 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 29, 29, 49, 49, 49, 49, 49, 50, 50, 49, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 18, 18, 49, 50, 50, 49, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576546714 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 Building ZINC001576546714 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576546714 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 17) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/17: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1) `ZINC001576546714.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576546714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001576546714 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 17, 17, 17, 17, 17, 17, 28, 28, 45, 45, 45, 45, 45, 50, 50, 45, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 17, 17, 45, 50, 50, 45, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 18) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/18: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1) `ZINC001576546714.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576546714.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001576546714 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCCN(C(=O)c2c[nH]c(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 8, 6, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 7, 18, 18, 18, 18, 18, 18, 29, 29, 49, 49, 49, 49, 49, 50, 50, 49, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 18, 18, 18, 18, 18, 18, 49, 50, 50, 49, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576546714 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576546714 Building ZINC001576587238 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576587238 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 19) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/19 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/19' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576587238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576587238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576587238 none Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 22, 12, 22, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 39, 39, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 165 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 20) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/20 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/20' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576587238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576587238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576587238 none Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 24, 16, 24, 16, 16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 40, 40, 16, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 162 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576587238 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 Building ZINC001576587238 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576587238 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 19) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576587238.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576587238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576587238 none Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 22, 12, 22, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 39, 39, 12, 12, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 165 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 20) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576587238.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576587238.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576587238 none Cn1cncc1CC(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 24, 16, 24, 16, 16, 16, 16, 6, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 40, 40, 16, 16, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 162 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576587238 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576587238 Building ZINC001576591147 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576591147 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 21) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/21 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/21' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576591147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591147 none C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 40, 40, 50, 50, 50, 19, 30, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 22) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/22 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/22' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576591147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591147 none C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 37, 37, 50, 50, 50, 19, 28, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576591147 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 Building ZINC001576591147 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576591147 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 21) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/21: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591147.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576591147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591147 none C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 40, 40, 50, 50, 50, 19, 30, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 40, 40, 40, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 190 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 22) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/22: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591147.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576591147.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591147 none C[C@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 37, 37, 50, 50, 50, 19, 28, 19, 19, 19, 19, 6, 19, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 37, 37, 37, 50, 50, 50, 50, 19, 19, 19, 19, 19, 19, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 189 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576591147 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591147 Building ZINC001576591148 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576591148 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 23) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/23 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/23' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576591148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591148 none C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 39, 39, 49, 50, 50, 20, 33, 20, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 39, 39, 39, 49, 49, 50, 50, 20, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 183 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 24) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/24 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/24' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576591148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591148 none C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 49, 50, 50, 15, 27, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 38, 38, 38, 49, 49, 50, 50, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 192 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576591148 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 Building ZINC001576591148 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576591148 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 23) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591148.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576591148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591148 none C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 33, 39, 39, 49, 50, 50, 20, 33, 20, 20, 20, 20, 7, 20, 4, 1, 4, 1, 1, 1, 1, 1, 1, 20, 39, 39, 39, 49, 49, 50, 50, 20, 20, 20, 20, 20, 20, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 183 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 24) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001576591148.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576591148.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576591148 none C[C@@H](CC(N)=O)C(=O)N1CCC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 38, 49, 50, 50, 15, 27, 15, 15, 15, 15, 5, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 38, 38, 38, 49, 49, 50, 50, 15, 15, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 192 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576591148 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576591148 Building ZINC001576711969 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576711969 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 25) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/25 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/25' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 37, 38, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 26) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/26 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/26' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 27) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/27 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/27' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 28) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/28 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/28' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 31, 21, 43, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 31, 31, 34, 34, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576711969 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 Building ZINC001576711969 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576711969 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 25) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 37, 38, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 26) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 27) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 28) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 31, 21, 43, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 31, 31, 34, 34, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576711969 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 Building ZINC001576711969 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576711969 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 25) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 37, 38, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 26) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 27) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 28) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 31, 21, 43, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 31, 31, 34, 34, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576711969 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 Building ZINC001576711969 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576711969 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 25) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 37, 38, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 26) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 27) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/27: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 30, 22, 42, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 30, 30, 33, 33, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 230 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 28) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/28: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1) `ZINC001576711969.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576711969.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001576711969 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1C[C@@H](NC(=O)CCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 6, 6, 6, 31, 21, 43, 50, 50, 50, 50, 50, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 6, 31, 31, 34, 34, 38, 37, 50, 2, 2] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 39, 34, 36, 38, 37, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576711969 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576711969 Building ZINC001576766131 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576766131 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 29) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/29 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/29' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576766131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766131 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 49, 23, 23, 23, 23, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 49, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 30) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/30 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/30' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576766131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766131 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576766131 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 Building ZINC001576766131 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576766131 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 29) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766131.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576766131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766131 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 49, 23, 23, 23, 23, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 49, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 30) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766131.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576766131.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766131 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576766131 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766131 Building ZINC001576766133 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576766133 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 31) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/31 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/31' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576766133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766133 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 32) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/32 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/32' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576766133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766133 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 49, 23, 23, 23, 23, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 49, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576766133 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 Building ZINC001576766133 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576766133 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 31) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576766133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766133 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 189 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 32) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1) `ZINC001576766133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576766133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576766133 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)Nc1cncc(c2nn[nH]n2)n1 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.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 8, 1, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 19, 9, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 30, 49, 49, 49, 49, 49, 50, 50, 50, 50, 50, 49, 23, 23, 23, 23, 22, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 49, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576766133 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576766133 Building ZINC001576767741 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767741 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 33) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/33 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/33' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 10, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 34) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/34 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/34' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 35) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/35 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/35' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 40, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 47, 47, 47, 47, 46, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 226 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 36) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/36 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/36' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 39, 39, 39, 39, 39, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 223 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767741 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 Building ZINC001576767741 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767741 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 33) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 10, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 34) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 35) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 40, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 47, 47, 47, 47, 46, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 226 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 36) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 39, 39, 39, 39, 39, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 223 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767741 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 Building ZINC001576767741 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767741 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 33) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 10, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 34) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 35) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 40, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 47, 47, 47, 47, 46, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 226 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 36) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 39, 39, 39, 39, 39, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 223 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767741 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 Building ZINC001576767741 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767741 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 33) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/33: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 10, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 34) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/34: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 35) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/35: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 14, 40, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 40, 46, 46, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 47, 47, 47, 47, 46, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 226 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 36) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/36: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767741.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767741.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767741 none CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 39, 39, 39, 39, 39, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 223 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767741 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767741 Building ZINC001576767742 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767742 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 37) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/37 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/37' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 38) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/38 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/38' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 11, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 39) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/39 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/39' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 38, 38, 38, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 218 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 40) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/40 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/40' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 14, 39, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 45, 47, 47, 47, 46, 47, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 231 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767742 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 Building ZINC001576767742 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767742 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 37) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 38) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 11, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 39) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 38, 38, 38, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 218 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 40) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 14, 39, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 45, 47, 47, 47, 46, 47, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 231 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767742 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 Building ZINC001576767742 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767742 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 37) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 38) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 11, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 39) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 38, 38, 38, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 218 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 40) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 14, 39, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 45, 47, 47, 47, 46, 47, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 231 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767742 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 Building ZINC001576767742 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001576767742 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 37) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 11, 34, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 38) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1/cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 11, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 35, 34, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 39) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/39: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 41, 41, 41, 41, 41, 41, 41, 50, 50, 50, 50, 50, 41, 38, 38, 38, 38, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 218 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 40) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/40: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1) `ZINC001576767742.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001576767742.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576767742 none CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)/N=c1\cc[nH]c(c2nn[nH]n2)n-1 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.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 1, 1, 8, 6, 1, 1, 8, 8, 8, 6, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 38, 14, 39, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 39, 45, 45, 45, 45, 45, 45, 45, 50, 50, 50, 50, 50, 45, 47, 47, 47, 46, 47, 14, 14, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 231 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576767742 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576767742 Building ZINC001576877557 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576877557 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 41) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/41 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/41' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001576877557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576877557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576877557 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 12, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 42) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/42 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/42' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001576877557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576877557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576877557 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 12, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576877557 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 Building ZINC001576877557 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576877557 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 41) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001576877557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576877557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576877557 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 12, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 42) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21) `ZINC001576877557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576877557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576877557 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccnc2ccnn21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 12, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001576877557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576877557 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877557 Building ZINC001576877987 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576877987 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 43) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/43 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/43' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001576877987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576877987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576877987 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 46, 50, 50, 50, 50, 50, 27, 27, 27, 19, 19, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 44) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/44 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/44' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001576877987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576877987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576877987 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 48, 50, 50, 50, 50, 50, 28, 28, 28, 19, 19, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576877987 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 Building ZINC001576877987 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576877987 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 43) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001576877987.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576877987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576877987 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 19, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 36, 36, 46, 50, 50, 50, 50, 50, 27, 27, 27, 19, 19, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 44) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O) `ZINC001576877987.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576877987.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576877987 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 19, 13, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 36, 36, 48, 50, 50, 50, 50, 50, 28, 28, 28, 19, 19, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576877987 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576877987 Building ZINC001576878068 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878068 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 45) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/45 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/45' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O) `ZINC001576878068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878068 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 38, 48, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 18, 18, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 46) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/46 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/46' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O) `ZINC001576878068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878068 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 49, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 16, 16, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878068 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 Building ZINC001576878068 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878068 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 45) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O) `ZINC001576878068.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878068 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 38, 48, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 18, 18, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 46) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O) `ZINC001576878068.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878068.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878068 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 49, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 16, 16, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878068 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878068 Building ZINC001576878069 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878069 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 47) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/47 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/47' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O) `ZINC001576878069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878069 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 49, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 16, 16, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 48) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/48 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/48' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O) `ZINC001576878069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878069 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 38, 48, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 18, 18, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878069 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 Building ZINC001576878069 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878069 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 47) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O) `ZINC001576878069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878069 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 34, 34, 49, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 16, 16, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 48) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O) `ZINC001576878069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576878069 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)C[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 15, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 38, 48, 50, 50, 50, 50, 50, 50, 50, 29, 29, 29, 18, 18, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878069 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878069 Building ZINC001576878076 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878076 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 49) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/49 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/49' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001576878076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001576878076 none COc1cnc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 50, 50, 46, 40, 46, 21, 40, 18, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 21, 21, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 50) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/50 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/50' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001576878076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001576878076 none COc1cnc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 50, 50, 45, 38, 45, 21, 38, 18, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 38, 38, 38, 21, 21, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878076 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 Building ZINC001576878076 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878076 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 49) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001576878076.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001576878076 none COc1cnc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 46, 50, 50, 46, 40, 46, 21, 40, 18, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 40, 40, 40, 21, 21, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 50) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1) `ZINC001576878076.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878076.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001576878076 none COc1cnc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 50, 50, 45, 38, 45, 21, 38, 18, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 38, 38, 38, 21, 21, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878076 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878076 Building ZINC001576878081 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878081 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 51) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/51 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/51' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1) `ZINC001576878081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878081 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 49, 49, 49, 49, 49, 50, 50, 49, 31, 31, 31, 18, 19, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 52) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/52 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/52' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1) `ZINC001576878081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878081 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 45, 45, 49, 49, 49, 49, 49, 50, 50, 49, 30, 30, 30, 17, 16, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878081 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 Building ZINC001576878081 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878081 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 51) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1) `ZINC001576878081.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878081 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 49, 49, 49, 49, 49, 50, 50, 49, 31, 31, 31, 18, 19, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 52) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1) `ZINC001576878081.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878081.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878081 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cncc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 17, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 45, 45, 49, 49, 49, 49, 49, 50, 50, 49, 30, 30, 30, 17, 16, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878081 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878081 Building ZINC001576878560 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878560 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 53) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/53 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/53' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001576878560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878560 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 49, 49, 49, 49, 50, 50, 49, 26, 26, 26, 13, 12, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 50, 50, 49] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 54) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/54 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/54' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001576878560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878560 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878560 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 Building ZINC001576878560 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878560 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 53) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001576878560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878560 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 49, 49, 49, 49, 50, 50, 49, 26, 26, 26, 13, 12, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 50, 50, 49] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 54) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1) `ZINC001576878560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576878560 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1coc(C(N)=O)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', '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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878560 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878560 Building ZINC001576878597 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878597 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 55) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/55 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/55' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1) `ZINC001576878597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576878597 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 33, 33, 38, 38, 50, 50, 50, 50, 50, 27, 27, 27, 14, 14, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 56) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/56 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/56' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1) `ZINC001576878597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576878597 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 33, 33, 38, 38, 50, 50, 50, 50, 50, 27, 27, 27, 14, 14, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878597 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 Building ZINC001576878597 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576878597 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 55) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1) `ZINC001576878597.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576878597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576878597 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 33, 33, 38, 38, 50, 50, 50, 50, 50, 27, 27, 27, 14, 14, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 56) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1) `ZINC001576878597.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576878597.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001576878597 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1ncccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 7, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 14, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 33, 33, 38, 38, 50, 50, 50, 50, 50, 27, 27, 27, 14, 14, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576878597 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576878597 Building ZINC001576879002 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879002 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 57) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/57 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/57' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879002 none CCCn1cc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 22, 22, 22, 18, 22, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 22, 22, 22, 18, 18, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 58) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/58 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/58' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879002 none CCCn1cc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 22, 22, 22, 18, 22, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 22, 22, 22, 18, 18, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879002 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 Building ZINC001576879002 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879002 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 57) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879002.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879002 none CCCn1cc(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 22, 22, 22, 18, 22, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 22, 22, 22, 18, 18, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 58) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879002.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879002.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879002 none CCCn1cc(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 29, 29, 22, 22, 22, 18, 22, 13, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 50, 50, 29, 22, 22, 22, 18, 18, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 246 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879002 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879002 Building ZINC001576879013 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879013 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 59) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/59 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/59' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001576879013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879013 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 18, 13, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 39, 39, 45, 45, 45, 50, 50, 45, 45, 45, 33, 33, 33, 17, 17, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 60) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/60 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/60' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001576879013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879013 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 18, 13, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 39, 39, 45, 45, 45, 50, 50, 45, 45, 45, 33, 33, 33, 17, 17, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879013 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 Building ZINC001576879013 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879013 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 59) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001576879013.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879013 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 18, 13, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 39, 39, 45, 45, 45, 50, 50, 45, 45, 45, 33, 33, 33, 17, 17, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 60) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1) `ZINC001576879013.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879013.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879013 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cc(C(N)=O)ccn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 11, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 18, 13, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 39, 39, 45, 45, 45, 50, 50, 45, 45, 45, 33, 33, 33, 17, 17, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 45, 45] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879013 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879013 Building ZINC001576879251 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879251 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 61) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/61 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/61' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001576879251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001576879251 none COc1c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 20, 32, 13, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 62) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/62 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/62' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001576879251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001576879251 none COc1c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 33, 13, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879251 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 Building ZINC001576879251 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879251 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 61) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001576879251.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001576879251 none COc1c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 20, 32, 13, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 62) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001576879251.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879251.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001576879251 none COc1c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 20, 33, 13, 20, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879251 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879251 Building ZINC001576879302 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879302 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 63) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/63 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/63' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1) `ZINC001576879302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879302 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 64) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/64 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/64' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1) `ZINC001576879302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879302 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 43, 43, 49, 49, 49, 49, 50, 50, 49, 49, 33, 33, 33, 19, 19, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879302 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 Building ZINC001576879302 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879302 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 63) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1) `ZINC001576879302.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879302 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 35, 35, 35, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 64) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1) `ZINC001576879302.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879302.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576879302 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(C(N)=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.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, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 11, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 21, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 43, 43, 49, 49, 49, 49, 50, 50, 49, 49, 33, 33, 33, 19, 19, 19, 19, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 50, 50, 49] 50 rigid atoms, others: [35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 43, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879302 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879302 Building ZINC001576879336 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879336 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 65) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/65 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/65' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001576879336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879336 none CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 16, 14, 16, 13, 14, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 27, 27, 27, 14, 14, 14, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 66) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/66 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/66' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001576879336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879336 none CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 15, 13, 15, 12, 13, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 26, 26, 26, 13, 13, 13, 12, 12, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879336 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 Building ZINC001576879336 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879336 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 65) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001576879336.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879336 none CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 16, 14, 16, 13, 14, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 27, 27, 27, 14, 14, 14, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 66) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001576879336.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879336.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879336 none CCn1nc(C)c(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 26, 26, 26, 26, 15, 13, 15, 12, 13, 9, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 26, 26, 26, 13, 13, 13, 12, 12, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 236 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879336 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879336 Building ZINC001576879772 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879772 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 67) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/67 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/67' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001576879772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576879772 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 12, 12, 14, 25, 25, 30, 30, 50, 50, 11, 11, 11, 9, 9, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 25, 25, 25, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 68) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/68 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/68' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001576879772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576879772 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 12, 12, 14, 25, 25, 30, 30, 50, 50, 11, 11, 11, 9, 9, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 25, 25, 25, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879772 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 Building ZINC001576879772 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879772 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 67) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001576879772.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576879772 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 12, 12, 14, 25, 25, 30, 30, 50, 50, 11, 11, 11, 9, 9, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 25, 25, 25, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 68) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1) `ZINC001576879772.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879772.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001576879772 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CN(C)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 5, 1, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 9, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 12, 12, 14, 25, 25, 30, 30, 50, 50, 11, 11, 11, 9, 9, 9, 9, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 25, 25, 25, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879772 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879772 Building ZINC001576879782 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879782 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 69) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/69 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/69' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879782 none CCn1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 26, 18, 17, 18, 10, 17, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50, 28, 26, 26, 17, 17, 17, 10, 10, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 70) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/70 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/70' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879782 none CCn1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 27, 18, 17, 18, 10, 17, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 29, 27, 27, 17, 17, 17, 10, 10, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879782 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 Building ZINC001576879782 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576879782 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 69) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879782.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576879782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879782 none CCn1cc(CC(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 28, 28, 28, 26, 18, 17, 18, 10, 17, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 50, 28, 26, 26, 17, 17, 17, 10, 10, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 70) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001576879782.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576879782.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001576879782 none CCn1cc(CC(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 29, 29, 27, 18, 17, 18, 10, 17, 8, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 29, 27, 27, 17, 17, 17, 10, 10, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 49, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576879782 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576879782 Building ZINC001576880312 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576880312 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 71) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/71 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/71' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576880312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576880312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576880312 none CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 36, 45, 21, 36, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 36, 21, 21, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 72) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/72 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/72' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576880312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576880312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576880312 none CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 36, 44, 18, 36, 12, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 36, 18, 18, 13, 13, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576880312 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 Building ZINC001576880312 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576880312 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 71) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576880312.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576880312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576880312 none CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 36, 45, 21, 36, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 36, 21, 21, 15, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 72) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001576880312.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576880312.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001576880312 none CNC(=O)C1(C(=O)N(C)CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 36, 44, 18, 36, 12, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 36, 36, 36, 18, 18, 13, 13, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 189 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576880312 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576880312 Building ZINC001576881224 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576881224 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 73) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/73 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/73' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001576881224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576881224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576881224 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 43, 43, 46, 46, 50, 50, 50, 50, 50, 37, 37, 37, 22, 22, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 74) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/74 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/74' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001576881224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576881224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576881224 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 43, 43, 46, 46, 50, 50, 50, 50, 50, 37, 37, 37, 22, 22, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576881224 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 Building ZINC001576881224 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576881224 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 73) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001576881224.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576881224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576881224 none CN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 43, 43, 46, 46, 50, 50, 50, 50, 50, 37, 37, 37, 22, 22, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 74) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C) `ZINC001576881224.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576881224.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001576881224 none CN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCc1cncn1C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.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', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 43, 43, 46, 46, 50, 50, 50, 50, 50, 37, 37, 37, 22, 22, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576881224 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576881224 Building ZINC001576951341 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576951341 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 75) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/75 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/75' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001576951341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576951341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951341 none CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 6, 10, 10, 10, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 10, 33, 33, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 76) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/76 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/76' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001576951341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576951341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951341 none CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 33, 33, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576951341 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 Building ZINC001576951341 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576951341 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 75) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001576951341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576951341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951341 none CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 6, 10, 10, 10, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 10, 33, 33, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 76) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001576951341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576951341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951341 none CN(CCCNC(=O)C[C@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 33, 33, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576951341 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951341 Building ZINC001576951342 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576951342 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 77) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/77 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/77' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001576951342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576951342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951342 none CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 32, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 78) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/78 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/78' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001576951342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576951342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951342 none CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 6, 10, 10, 10, 41, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 10, 36, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576951342 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 Building ZINC001576951342 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001576951342 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 77) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/77: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001576951342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001576951342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951342 none CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 32, 32, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 167 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 78) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/78: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001576951342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001576951342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001576951342 none CN(CCCNC(=O)C[C@@H]1COC(=O)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 6, 10, 10, 10, 41, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 10, 36, 36, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001576951342 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001576951342 Building ZINC001577067392 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577067392 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 79) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/79 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/79' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001577067392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577067392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577067392 none CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 23, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 23, 23, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 80) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/80 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/80' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001577067392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577067392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577067392 none CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 24, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 24, 24, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577067392 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 Building ZINC001577067392 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577067392 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 79) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001577067392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577067392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577067392 none CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 23, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 23, 23, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 80) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1) `ZINC001577067392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577067392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577067392 none CN(C)c1cnc(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 1, 8, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 48, 48, 48, 24, 10, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 24, 24, 11, 11, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577067392 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577067392 Building ZINC001577092482 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577092482 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 81) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/81 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/81' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577092482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577092482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092482 none CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 13, 19, 43, 43, 46, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 13, 13, 19, 19, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 82) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/82 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/82' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577092482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577092482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092482 none CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 12, 20, 40, 40, 46, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 12, 12, 20, 20, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577092482 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 Building ZINC001577092482 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577092482 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 81) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577092482.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577092482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092482 none CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 13, 19, 43, 43, 46, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 13, 13, 19, 19, 43, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 82) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577092482.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577092482.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092482 none CN(CCCNC(=O)[C@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 10, 12, 20, 40, 40, 46, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 10, 10, 12, 12, 20, 20, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577092482 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092482 Building ZINC001577092484 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577092484 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 83) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/83 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/83' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577092484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577092484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092484 none CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 13, 21, 40, 40, 46, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 13, 13, 21, 21, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 84) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/84 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/84' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577092484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577092484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092484 none CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 13, 20, 42, 42, 45, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 13, 13, 20, 20, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577092484 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 Building ZINC001577092484 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577092484 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 83) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577092484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577092484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092484 none CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 13, 21, 40, 40, 46, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 13, 13, 21, 21, 40, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 84) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577092484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577092484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577092484 none CN(CCCNC(=O)[C@@H]1CCCS1(=O)=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'S.o2', 'O.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 14, 11, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 3, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 11, 13, 20, 42, 42, 45, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 11, 13, 13, 20, 20, 42, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 186 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577092484 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577092484 Building ZINC001577113369 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577113369 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 85) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/85 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/85' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577113369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577113369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577113369 none CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 6, 11, 23, 23, 23, 44, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 6, 6, 11, 11, 23, 44, 44, 47, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 86) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/86 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/86' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577113369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577113369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577113369 none CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 5, 10, 22, 22, 22, 44, 46, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 10, 10, 22, 44, 44, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577113369 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 Building ZINC001577113369 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577113369 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 85) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577113369.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577113369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577113369 none CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 6, 11, 23, 23, 23, 44, 47, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 6, 6, 11, 11, 23, 44, 44, 47, 47, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 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/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 86) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577113369.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577113369.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577113369 none CN(CCCNC(=O)CCc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 5, 5, 10, 22, 22, 22, 44, 46, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 5, 5, 5, 5, 10, 10, 22, 44, 44, 46, 46, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577113369 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577113369 Building ZINC001577119390 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577119390 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 87) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/87 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/87' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577119390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577119390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119390 none CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 20, 25, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 20, 20, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 88) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/88 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/88' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577119390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577119390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119390 none CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 16, 18, 23, 32, 32, 37, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 18, 18, 23, 23, 32, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577119390 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 Building ZINC001577119390 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577119390 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 87) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577119390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577119390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119390 none CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 20, 25, 36, 36, 37, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 20, 20, 25, 25, 36, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 88) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577119390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577119390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119390 none CN(CCCNC(=O)[C@@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 16, 18, 23, 32, 32, 37, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 18, 18, 23, 23, 32, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577119390 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119390 Building ZINC001577119392 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577119392 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 89) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/89 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/89' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577119392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577119392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119392 none CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 19, 24, 34, 34, 38, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 19, 19, 24, 24, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 90) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/90 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/90' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577119392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577119392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119392 none CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 16, 19, 23, 33, 33, 35, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 19, 19, 23, 23, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577119392 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 Building ZINC001577119392 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577119392 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 89) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577119392.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577119392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119392 none CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 19, 24, 34, 34, 38, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 19, 19, 24, 24, 34, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 90) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577119392.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577119392.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577119392 none CN(CCCNC(=O)[C@H]1CCCNC1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 3, 7, 16, 19, 23, 33, 33, 35, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 19, 19, 23, 23, 33, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577119392 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577119392 Building ZINC001577123696 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577123696 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 91) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/91 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/91' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577123696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577123696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123696 none CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 7, 12, 12, 12, 42, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 6, 6, 7, 7, 12, 38, 38, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 92) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/92 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/92' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577123696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577123696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123696 none CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 6, 12, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577123696 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 Building ZINC001577123696 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577123696 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 91) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577123696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577123696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123696 none CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 7, 12, 12, 12, 42, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 6, 6, 7, 7, 12, 38, 38, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 92) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577123696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577123696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123696 none CN(CCCNC(=O)C[C@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 6, 12, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 6, 6, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 176 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577123696 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123696 Building ZINC001577123697 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577123697 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 93) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/93 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/93' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577123697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577123697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123697 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 7, 12, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 6, 6, 7, 7, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 94) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/94 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/94' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577123697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577123697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123697 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 7, 12, 12, 12, 41, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 6, 6, 7, 7, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577123697 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 Building ZINC001577123697 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577123697 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 93) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577123697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577123697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123697 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 7, 12, 12, 12, 45, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 6, 6, 7, 7, 12, 41, 41, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 94) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577123697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577123697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577123697 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 8, 5, 1, 11, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 6, 7, 12, 12, 12, 41, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 6, 6, 7, 7, 12, 37, 37, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577123697 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577123697 Building ZINC001577161726 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577161726 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 95) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/95 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/95' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001577161726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577161726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577161726 none CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 27, 27, 27, 16, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 16, 16, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 96) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/96 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/96' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001577161726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577161726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577161726 none CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 27, 27, 27, 16, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 16, 16, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577161726 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 Building ZINC001577161726 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577161726 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 95) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001577161726.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577161726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577161726 none CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 27, 27, 27, 16, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 16, 16, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 96) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001577161726.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577161726.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577161726 none CCn1nc(C)c(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 27, 27, 27, 27, 27, 27, 27, 27, 16, 9, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 27, 27, 27, 27, 16, 16, 9, 9, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577161726 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577161726 Building ZINC001577186710 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577186710 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 97) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/97 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/97' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577186710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577186710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001577186710 none CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 11, 7, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 46, 50, 50, 50, 50, 26, 11, 11, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 98) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/98 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/98' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577186710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577186710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001577186710 none CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 24, 24, 24, 9, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 24, 9, 9, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577186710 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 Building ZINC001577186710 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577186710 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 97) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577186710.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577186710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001577186710 none CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 26, 26, 11, 7, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 46, 46, 50, 50, 50, 50, 26, 11, 11, 7, 7, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 98) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577186710.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577186710.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001577186710 none CNC(=O)C1(C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 24, 24, 24, 9, 6, 5, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 45, 45, 50, 50, 50, 50, 24, 9, 9, 6, 6, 5, 5, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577186710 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577186710 Building ZINC001577209723 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209723 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 99) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/99 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/99' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 100) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/100 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/100' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 101) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/101 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/101' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 102) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/102 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/102' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209723 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 Building ZINC001577209723 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209723 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 99) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 100) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 101) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 102) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209723 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 Building ZINC001577209723 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209723 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 99) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 100) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 101) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 102) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209723 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 Building ZINC001577209723 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209723 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 99) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 100) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 101) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/101: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 7, 7, 7, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 7, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 102) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/102: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209723.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209723.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209723 none CN(CCCNC(=O)C[C@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 39, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209723 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209723 Building ZINC001577209724 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209724 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 103) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/103 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/103' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 104) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/104 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/104' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 105) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/105 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/105' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 106) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/106 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/106' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209724 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 Building ZINC001577209724 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209724 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 103) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 104) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 105) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 106) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209724 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 Building ZINC001577209724 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209724 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 103) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 104) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 105) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 106) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209724 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 Building ZINC001577209724 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577209724 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 103) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 104) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 105) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/105: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 9, 9, 9, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 9, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 106) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/106: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -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(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577209724.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577209724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 57 natoms 56 natoms 55 natoms 54 names: ZINC001577209724 none CN(CCCNC(=O)C[C@@H]1CCN(C)C1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 5, 10, 5, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 2, 4, 4, 5, 8, 8, 8, 40, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 4, 4, 5, 5, 8, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577209724 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577209724 Building ZINC001577224749 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577224749 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 107) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/107 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/107' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577224749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577224749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577224749 none CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 108) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/108 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/108' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577224749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577224749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577224749 none CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577224749 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 Building ZINC001577224749 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577224749 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 107) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577224749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577224749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577224749 none CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 19, 19, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 108) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577224749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577224749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001577224749 none CN(CCCNC(=O)c1cn(C)ccc1=O)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 1, 11, 5, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 20, 20, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577224749 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577224749 Building ZINC001577265164 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577265164 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 109) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/109 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/109' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577265164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577265164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577265164 none CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 7, 11, 11, 11, 36, 40, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 7, 7, 11, 36, 36, 40, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 110) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/110 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/110' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577265164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577265164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577265164 none CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 5, 8, 12, 12, 12, 35, 39, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 8, 7, 12, 35, 35, 39, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577265164 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 Building ZINC001577265164 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577265164 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 109) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577265164.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577265164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577265164 none CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 5, 5, 7, 11, 11, 11, 36, 40, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 5, 5, 7, 7, 11, 36, 36, 40, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 110) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577265164.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577265164.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577265164 none CN(CCCNC(=O)CCc1cncn1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 5, 1, 11, 5, 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, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 6, 5, 8, 12, 12, 12, 35, 39, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 8, 7, 12, 35, 35, 39, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577265164 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577265164 Building ZINC001577288394 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577288394 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 111) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/111 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/111' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577288394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577288394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288394 none CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 8, 10, 20, 30, 30, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 11, 11, 19, 20, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 112) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/112 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/112' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577288394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577288394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288394 none CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 8, 16, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 9, 16, 15, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577288394 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 Building ZINC001577288394 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577288394 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 111) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577288394.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577288394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288394 none CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 8, 10, 20, 30, 30, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 8, 8, 11, 11, 19, 20, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 112) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577288394.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577288394.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288394 none CN(CCCNC(=O)[C@@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 8, 16, 30, 30, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 9, 9, 16, 15, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577288394 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288394 Building ZINC001577288395 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577288395 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 113) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/113 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/113' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577288395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577288395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288395 none CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 31, 31, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 17, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 114) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/114 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/114' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577288395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577288395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288395 none CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 19, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 19, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577288395 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 Building ZINC001577288395 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577288395 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 113) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577288395.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577288395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288395 none CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 18, 31, 31, 37, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 17, 18, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 114) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577288395.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577288395.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577288395 none CN(CCCNC(=O)[C@]1(C)CCC(=O)NC1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 9, 19, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 10, 10, 19, 18, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577288395 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577288395 Building ZINC001577401244 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401244 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 115) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/115 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/115' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401244 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 116) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/116 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/116' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401244 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 39, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401244 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 Building ZINC001577401244 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401244 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 115) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401244 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 116) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401244 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 39, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401244 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401244 Building ZINC001577401245 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401245 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 117) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/117 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/117' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401245 none C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 39, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 118) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/118 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/118' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401245 none C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401245 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 Building ZINC001577401245 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401245 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 117) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401245.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401245 none C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 50, 39, 39, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 39, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 118) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401245.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401245.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401245 none C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 50, 37, 37, 19, 9, 8, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 37, 19, 19, 10, 10, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401245 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401245 Building ZINC001577401246 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401246 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 119) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/119 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/119' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401246 none C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 27, 47, 27, 27, 15, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 27, 15, 15, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 120) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/120 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/120' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401246 none C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 25, 25, 14, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 25, 14, 14, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401246 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 Building ZINC001577401246 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401246 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 119) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401246.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401246 none C[C@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 27, 47, 27, 27, 15, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 27, 15, 15, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 120) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1) `ZINC001577401246.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401246.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401246 none C[C@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 25, 25, 14, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 25, 14, 14, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401246 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401246 Building ZINC001577401247 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401247 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 121) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/121 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/121' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401247 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 25, 25, 14, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 25, 14, 14, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 122) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/122 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/122' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401247 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 27, 47, 27, 27, 15, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 27, 15, 15, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401247 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 Building ZINC001577401247 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577401247 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 121) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577401247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401247 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 25, 25, 14, 7, 6, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 50, 50, 50, 49, 49, 49, 25, 14, 14, 7, 7, 6, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 218 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 122) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1) `ZINC001577401247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577401247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 13 0 4 13 1 4 13 2 3 13 2 16 to be deleted 17 to be deleted 18 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577401247 none C[C@@H](C(=O)NCCCN(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 1, 11, 8, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 27, 47, 27, 27, 15, 8, 7, 3, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50, 47, 47, 47, 27, 15, 15, 8, 8, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 39, 40, 41, 42, 11, 44, 13, 14, 15, 16, 17, 18, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577401247 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577401247 Building ZINC001577424729 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424729 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 123) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/123 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/123' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424729 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 124) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/124 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/124' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424729 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424729 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 Building ZINC001577424729 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424729 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 123) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424729.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424729 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 124) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424729.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424729.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424729 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 133 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424729 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424729 Building ZINC001577424730 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424730 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 125) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/125 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/125' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424730 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 30, 30, 50, 50, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 126) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/126 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/126' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424730 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424730 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 Building ZINC001577424730 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424730 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 125) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424730.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424730 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 1, 1, 1, 7, 12, 12, 12, 12, 12, 12, 12, 30, 30, 50, 50, 50, 50, 50, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 126) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424730.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424730.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424730 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 31, 31, 50, 50, 50, 50, 50, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424730 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424730 Building ZINC001577424731 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424731 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 127) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/127 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/127' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424731 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 128) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/128 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/128' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424731 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424731 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 Building ZINC001577424731 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424731 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 127) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424731.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424731 none C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 3, 1, 3, 1, 1, 1, 1, 1, 1, 6, 12, 12, 12, 12, 12, 12, 12, 29, 29, 50, 50, 50, 50, 50, 6, 6, 6, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12, 12, 12, 12, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 134 number of broken/clashed sets: 26 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 128) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424731.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424731.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424731 none C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 14, 14, 14, 14, 14, 14, 14, 28, 28, 50, 50, 50, 50, 50, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14, 14, 14, 14, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 130 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424731 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424731 Building ZINC001577424732 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424732 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 129) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/129 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/129' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424732 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 130) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/130 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/130' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424732 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424732 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 Building ZINC001577424732 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577424732 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 129) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424732.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577424732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424732 none C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 2, 1, 2, 1, 1, 1, 2, 2, 2, 5, 13, 13, 13, 13, 13, 13, 13, 27, 27, 50, 50, 50, 50, 50, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 13, 13, 13, 13, 13, 13, 13, 13, 50, 50, 50, 50] 50 rigid atoms, others: [8, 4, 6, 7] set([0, 1, 2, 3, 5, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 130) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1) `ZINC001577424732.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577424732.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 6 is the cov attach 4 6 0 4 6 1 4 6 2 3 6 2 9 to be deleted 10 to be deleted 11 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577424732 none C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCCN1C(=O)c1ncn(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 8, 7, 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, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 11, 11, 11, 11, 11, 11, 11, 27, 27, 50, 50, 50, 50, 50, 5, 5, 5, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 11, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 37, 6, 7, 8, 9, 10, 11, 36, 38, 39, 31] set([0, 1, 2, 3, 5, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577424732 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577424732 Building ZINC001577493130 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577493130 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 131) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/131 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/131' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577493130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577493130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577493130 none CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 11, 11, 11, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 11, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 50, 51, 49, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 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/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 132) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/132 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/132' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577493130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577493130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577493130 none CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 10, 10, 10, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 10, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 50, 51, 49, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 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/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577493130 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 Building ZINC001577493130 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577493130 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 131) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577493130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577493130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577493130 none CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 11, 11, 11, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 11, 29, 29, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 50, 51, 49, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 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/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 132) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577493130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577493130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577493130 none CCN(CCCNC(=O)Cc1cnn(C)c1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 1, 8, 8, 5, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 10, 10, 10, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 10, 28, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 50, 51, 49, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 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/167320/xcr-8058097.70/working/building/ZINC001577493130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577493130 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577493130 Building ZINC001577500762 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500762 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 133) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/133 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/133' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1) `ZINC001577500762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500762 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 17, 17, 29, 36, 50, 50, 50, 50, 14, 14, 14, 14, 14, 9, 9, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 36, 36, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 134) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/134 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/134' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1) `ZINC001577500762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500762 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 29, 36, 50, 50, 50, 50, 13, 13, 13, 13, 13, 8, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 36, 36, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500762 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 Building ZINC001577500762 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500762 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 133) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1) `ZINC001577500762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500762 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 17, 17, 29, 36, 50, 50, 50, 50, 14, 14, 14, 14, 14, 9, 9, 9, 9, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 36, 36, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 134) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1) `ZINC001577500762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500762 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)CCn1cnnn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 8, 1, 8, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 6, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 29, 36, 50, 50, 50, 50, 13, 13, 13, 13, 13, 8, 8, 8, 8, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 36, 36, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 194 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500762 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500762 Building ZINC001577500814 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500814 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 135) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/135 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/135' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O) `ZINC001577500814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500814 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 24, 19, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 42, 44, 49, 49, 49, 49, 49, 49, 49, 40, 40, 40, 40, 40, 24, 24, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 136) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/136 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/136' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O) `ZINC001577500814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500814 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 41, 44, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 23, 23, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500814 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 Building ZINC001577500814 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500814 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 135) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/135: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O) `ZINC001577500814.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500814 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 24, 19, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 42, 44, 49, 49, 49, 49, 49, 49, 49, 40, 40, 40, 40, 40, 24, 24, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 136) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/136: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O) `ZINC001577500814.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500814.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500814 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 41, 44, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 23, 23, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500814 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500814 Building ZINC001577500815 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500815 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 137) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/137 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/137' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O) `ZINC001577500815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500815 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 41, 44, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 23, 23, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 138) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/138 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/138' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O) `ZINC001577500815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500815 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 24, 19, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 42, 44, 49, 49, 49, 49, 49, 49, 49, 40, 40, 40, 40, 40, 24, 24, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500815 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 Building ZINC001577500815 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500815 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 137) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O) `ZINC001577500815.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500815 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 23, 19, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 41, 44, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 41, 41, 23, 23, 21, 21, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 252 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 138) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O) `ZINC001577500815.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500815.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500815 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CCN(C)C1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 33, 24, 19, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 42, 44, 49, 49, 49, 49, 49, 49, 49, 40, 40, 40, 40, 40, 24, 24, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 250 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500815 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500815 Building ZINC001577500824 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500824 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 139) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/139 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/139' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1) `ZINC001577500824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500824 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 6, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 19, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 49, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 30, 19, 19, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 140) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/140 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/140' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1) `ZINC001577500824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500824 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 6, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 20, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 20, 20, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500824 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 Building ZINC001577500824 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500824 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 139) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1) `ZINC001577500824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500824 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 6, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 26, 19, 14, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 49, 49, 49, 49, 49, 49, 49, 30, 30, 30, 30, 30, 19, 19, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 140) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1) `ZINC001577500824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 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: ZINC001577500824 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1c[nH]c(=O)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.am', 'H', 'C.2', 'O.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 6, 1, 11, 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] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 27, 20, 15, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 38, 38, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30, 30, 20, 20, 18, 18, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500824 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500824 Building ZINC001577500917 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500917 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 141) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/141 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/141' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001577500917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500917 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 44, 45, 46, 46, 46, 46, 46, 46, 46, 41, 41, 41, 41, 41, 25, 25, 24, 24, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 142) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/142 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/142' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001577500917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500917 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 36, 26, 21, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 44, 45, 45, 45, 45, 45, 45, 45, 45, 42, 42, 42, 42, 42, 26, 26, 25, 25, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500917 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 Building ZINC001577500917 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500917 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 141) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001577500917.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500917 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 36, 25, 20, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 44, 45, 46, 46, 46, 46, 46, 46, 46, 41, 41, 41, 41, 41, 25, 25, 24, 24, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 229 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 142) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1) `ZINC001577500917.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500917.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500917 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [42, 36, 26, 21, 16, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 44, 45, 45, 45, 45, 45, 45, 45, 45, 42, 42, 42, 42, 42, 26, 26, 25, 25, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45, 45, 45, 45, 45, 45] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 231 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500917 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500917 Building ZINC001577500918 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500918 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 143) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/143 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/143' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1) `ZINC001577500918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500918 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 25, 18, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 41, 43, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 18, 18, 17, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 144) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/144 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/144' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1) `ZINC001577500918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500918 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 41, 43, 43, 43, 43, 43, 43, 43, 31, 31, 31, 31, 31, 16, 16, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500918 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 Building ZINC001577500918 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577500918 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 143) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1) `ZINC001577500918.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577500918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500918 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 25, 18, 15, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 41, 43, 43, 43, 43, 43, 43, 43, 32, 32, 32, 32, 32, 18, 18, 17, 17, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 202 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 144) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1) `ZINC001577500918.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577500918.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577500918 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@H]1CC(=O)N(C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 7, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 24, 16, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 41, 43, 43, 43, 43, 43, 43, 43, 31, 31, 31, 31, 31, 16, 16, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577500918 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577500918 Building ZINC001577501022 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577501022 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 145) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/145 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/145' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1) `ZINC001577501022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577501022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501022 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 18, 17, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 41, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 18, 18, 18, 18, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 146) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/146 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/146' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1) `ZINC001577501022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577501022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501022 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 17, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 17, 17, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 203 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577501022 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 Building ZINC001577501022 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577501022 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 145) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1) `ZINC001577501022.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577501022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501022 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 18, 17, 14, 2, 2, 1, 2, 1, 1, 1, 2, 2, 2, 41, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 18, 18, 18, 18, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [9, 10, 11, 7] set([0, 1, 2, 3, 4, 5, 6, 8, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 146) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1) `ZINC001577501022.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577501022.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501022 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 17, 17, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 17, 17, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 203 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577501022 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501022 Building ZINC001577501023 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577501023 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 147) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/147 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/147' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1) `ZINC001577501023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577501023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501023 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 17, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 17, 17, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 148) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/148 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/148' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1) `ZINC001577501023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577501023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501023 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 17, 16, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 17, 17, 17, 17, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577501023 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 Building ZINC001577501023 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577501023 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 147) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/147: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1) `ZINC001577501023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577501023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501023 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 42, 17, 16, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 47, 17, 17, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 207 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 148) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/148: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1) `ZINC001577501023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577501023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577501023 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)[C@@]1(C)CNC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 5, 5, 8, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 41, 17, 16, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 46, 46, 46, 17, 17, 17, 17, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577501023 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501023 Building ZINC001577501191 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577501191 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 149) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/149 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/149' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O) `ZINC001577501191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577501191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577501191 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 13, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 29, 29, 38, 43, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 150) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/150 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/150' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O) `ZINC001577501191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577501191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577501191 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 13, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 38, 43, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577501191 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 Building ZINC001577501191 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577501191 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 149) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O) `ZINC001577501191.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577501191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577501191 none CCN(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 13, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 29, 29, 38, 43, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 150) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O) `ZINC001577501191.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577501191.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 9 is the cov attach 4 9 0 4 9 1 4 9 2 3 9 2 12 to be deleted 13 to be deleted 14 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577501191 none CCN(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 24, 13, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 30, 30, 38, 43, 43, 43, 43, 43, 43, 30, 30, 30, 30, 30, 13, 13, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 43, 43, 43, 43] 50 rigid atoms, others: [45, 43, 37, 38, 7, 40, 9, 10, 11, 12, 13, 14, 44, 41, 39, 42] set([0, 1, 2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577501191 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577501191 Building ZINC001577617711 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577617711 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 151) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/151 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/151' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577617711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577617711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577617711 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 6, 9, 13, 32, 32, 40, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 9, 9, 13, 13, 32, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 152) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/152 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/152' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577617711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577617711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577617711 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 7, 10, 14, 33, 33, 37, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 10, 10, 14, 14, 33, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577617711 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 Building ZINC001577617711 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577617711 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 151) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577617711.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577617711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577617711 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 6, 9, 13, 32, 32, 40, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 6, 6, 9, 9, 13, 13, 32, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 152) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577617711.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577617711.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577617711 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [7, 5, 2, 5, 7, 10, 14, 33, 33, 37, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 10, 10, 14, 14, 33, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577617711 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577617711 Building ZINC001577635049 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577635049 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 153) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/153 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/153' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577635049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577635049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577635049 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 9, 12, 18, 35, 35, 37, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 12, 12, 18, 18, 35, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 154) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/154 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/154' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577635049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577635049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577635049 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 10, 13, 19, 35, 35, 38, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 13, 13, 19, 19, 35, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577635049 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 Building ZINC001577635049 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577635049 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 153) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577635049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577635049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577635049 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 5, 9, 12, 18, 35, 35, 37, 48, 48, 48, 48, 48, 48, 48, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 9, 9, 12, 12, 18, 18, 35, 48, 48, 48, 48, 48, 48, 48, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 154) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577635049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577635049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577635049 none CCN(CCCNC(=O)[C@@H]1CCC(=O)N1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 6, 10, 13, 19, 35, 35, 38, 47, 47, 47, 47, 47, 47, 47, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 10, 10, 13, 13, 19, 19, 35, 47, 47, 47, 47, 47, 47, 47, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577635049 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577635049 Building ZINC001577653706 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577653706 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 155) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/155 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/155' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577653706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577653706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577653706 none CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 8, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 4, 4, 5, 12, 12, 12, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 5, 5, 12, 41, 41, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 156) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/156 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/156' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577653706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577653706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577653706 none CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 8, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 11, 11, 11, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 11, 41, 41, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577653706 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 Building ZINC001577653706 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577653706 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 155) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001577653706.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577653706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577653706 none CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 8, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 4, 4, 5, 12, 12, 12, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 4, 4, 4, 4, 5, 5, 12, 41, 41, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 156) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001577653706.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577653706.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577653706 none CCN(CCCNC(=O)Cc1nonc1C)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 5, 5, 5, 8, 1, 11, 5, 1, 8, 12, 8, 1, 5, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 3, 3, 4, 11, 11, 11, 41, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3, 3, 3, 4, 4, 11, 41, 41, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 2, 49, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23] set([0, 1, 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, 38, 39, 40]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577653706 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577653706 Building ZINC001577720230 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720230 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 157) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/157 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/157' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720230 none CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 48, 40, 47, 27, 22, 27, 12, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 25, 25, 48, 48, 48, 47, 47, 47, 40, 40, 12, 11, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 158) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/158 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/158' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720230 none CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 48, 38, 44, 27, 23, 27, 14, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 28, 28, 48, 48, 48, 44, 44, 44, 38, 38, 13, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720230 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 Building ZINC001577720230 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720230 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 157) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720230.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720230 none CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 47, 48, 40, 47, 27, 22, 27, 12, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 25, 25, 48, 48, 48, 47, 47, 47, 40, 40, 12, 11, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 158) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720230.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720230.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720230 none CC(=O)N(C)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [48, 44, 48, 38, 44, 27, 23, 27, 14, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 28, 28, 48, 48, 48, 44, 44, 44, 38, 38, 13, 13, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720230 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720230 Building ZINC001577720620 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720620 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 159) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/159 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/159' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1) `ZINC001577720620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577720620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 10, 21, 25, 25, 46, 49, 49, 49, 21, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 10, 10, 46, 46, 49, 49, 49, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 248 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 160) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/160 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/160' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1) `ZINC001577720620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577720620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 7, 12, 20, 26, 26, 42, 47, 47, 47, 20, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 9, 9, 12, 12, 42, 42, 47, 47, 47, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 250 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720620 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 Building ZINC001577720620 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720620 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 159) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1) `ZINC001577720620.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577720620 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 7, 10, 21, 25, 25, 46, 49, 49, 49, 21, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 8, 8, 10, 10, 46, 46, 49, 49, 49, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 32, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 248 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 160) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1) `ZINC001577720620.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720620.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577720620 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CS(C)(=O)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 14, 5, 11, 11, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 7, 12, 20, 26, 26, 42, 47, 47, 47, 20, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 9, 9, 12, 12, 42, 42, 47, 47, 47, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 23, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 250 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720620 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720620 Building ZINC001577720693 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720693 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 161) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/161 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/161' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1) `ZINC001577720693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720693 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 20, 29, 30, 30, 37, 46, 50, 50, 50, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 20, 20, 37, 37, 46, 46, 50, 50, 50, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 162) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/162 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/162' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1) `ZINC001577720693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720693 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 19, 27, 28, 28, 36, 45, 50, 50, 50, 27, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 19, 19, 36, 36, 45, 45, 50, 50, 50, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720693 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 Building ZINC001577720693 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720693 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 161) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/161: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1) `ZINC001577720693.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720693 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 13, 20, 29, 30, 30, 37, 46, 50, 50, 50, 29, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 13, 13, 20, 20, 37, 37, 46, 46, 50, 50, 50, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 219 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 162) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/162: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1) `ZINC001577720693.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720693.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720693 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCCN(C(=O)CCNC(N)=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 8, 11, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 12, 19, 27, 28, 28, 36, 45, 50, 50, 50, 27, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 12, 12, 19, 19, 36, 36, 45, 45, 50, 50, 50, 28, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 223 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720693 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720693 Building ZINC001577720701 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720701 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 163) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/163 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/163' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720701 none C[C@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 31, 37, 16, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 40, 40, 44, 45, 45, 45, 45, 44, 44, 44, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 45, 45] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 164) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/164 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/164' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720701 none C[C@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 28, 35, 13, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 38, 38, 44, 45, 45, 45, 45, 44, 44, 44, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 45, 45] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720701 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 Building ZINC001577720701 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720701 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 163) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720701 none C[C@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 31, 37, 16, 12, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 40, 40, 44, 45, 45, 45, 45, 44, 44, 44, 16, 16, 14, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 45, 45] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 226 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 164) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720701 none C[C@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 44, 28, 35, 13, 9, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 38, 38, 44, 45, 45, 45, 45, 44, 44, 44, 13, 13, 11, 11, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 38, 38, 38, 38, 45, 45] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 221 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720701 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720701 Building ZINC001577720702 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720702 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 165) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/165 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/165' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720702 none C[C@@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 27, 34, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 37, 44, 46, 46, 46, 46, 44, 44, 44, 16, 16, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 46, 46] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 166) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/166 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/166' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720702 none C[C@@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 43, 29, 35, 18, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 40, 40, 43, 46, 46, 46, 46, 43, 43, 43, 18, 18, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 46, 46] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720702 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 Building ZINC001577720702 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720702 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 165) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720702.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720702 none C[C@@H](C(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 44, 27, 34, 16, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 37, 37, 44, 46, 46, 46, 46, 44, 44, 44, 16, 16, 13, 13, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37, 37, 37, 37, 46, 46] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 231 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 166) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1) `ZINC001577720702.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720702.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577720702 none C[C@@H](C(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1)n1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 8, 1, 8, 7, 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, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 35, 43, 29, 35, 18, 13, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 40, 40, 43, 46, 46, 46, 46, 43, 43, 43, 18, 18, 14, 14, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 40, 40, 40, 46, 46] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 10, 43, 12, 13, 14, 15, 16, 17, 44, 42] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 243 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720702 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720702 Building ZINC001577720740 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720740 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 167) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/167 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/167' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001577720740 none CNC(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 49, 30, 23, 30, 12, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 30, 49, 49, 49, 49, 46, 46, 12, 12, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 168) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/168 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/168' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001577720740 none CNC(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 48, 30, 24, 30, 13, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 29, 29, 48, 48, 48, 48, 46, 46, 13, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720740 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 Building ZINC001577720740 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720740 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 167) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720740.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001577720740 none CNC(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 49, 30, 23, 30, 12, 8, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 30, 30, 49, 49, 49, 49, 46, 46, 12, 12, 9, 9, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 234 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 168) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720740.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720740.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001577720740 none CNC(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 46, 48, 30, 24, 30, 13, 8, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 29, 29, 48, 48, 48, 48, 46, 46, 13, 13, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 223 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720740 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720740 Building ZINC001577720799 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720799 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 169) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/169 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/169' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720799 none CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 29, 25, 29, 13, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 27, 27, 50, 50, 50, 50, 50, 50, 47, 47, 13, 12, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 170) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/170 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/170' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720799 none CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 43, 47, 26, 23, 26, 14, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 25, 25, 47, 47, 47, 47, 47, 47, 43, 43, 14, 14, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720799 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 Building ZINC001577720799 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577720799 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 169) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720799.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577720799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720799 none CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 29, 25, 29, 13, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 27, 27, 50, 50, 50, 50, 50, 50, 47, 47, 13, 12, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27, 27, 27, 27] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 220 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 170) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001577720799.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577720799.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577720799 none CN(C)C(=O)CC(=O)N(CCCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [47, 47, 47, 43, 47, 26, 23, 26, 14, 11, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 25, 25, 47, 47, 47, 47, 47, 47, 43, 43, 14, 14, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25] 50 rigid atoms, others: [45, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 206 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577720799 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577720799 Building ZINC001577813781 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577813781 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 171) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/171 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/171' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001577813781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577813781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577813781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 7, 7, 7, 30, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 7, 30, 30, 39, 39, 50, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 47, 48, 49, 50, 51] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 172) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/172 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/172' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001577813781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577813781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577813781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 14, 14, 14, 38, 41, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 14, 38, 38, 41, 41, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577813781 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 Building ZINC001577813781 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577813781 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 171) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001577813781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577813781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577813781 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 7, 7, 7, 30, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 4, 4, 7, 30, 30, 39, 39, 50, 1, 1, 1, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 47, 48, 49, 50, 51] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 172) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1) `ZINC001577813781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577813781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577813781 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N(CCCNC(=O)CCc1cnn[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 5, 1, 1, 8, 8, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 7, 14, 14, 14, 38, 41, 50, 50, 50, 50, 50, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 7, 7, 14, 38, 38, 41, 41, 50, 2, 2, 2, 2, 2] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577813781 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577813781 Building ZINC001577824462 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577824462 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 173) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/173 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/173' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1) `ZINC001577824462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577824462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577824462 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 12, 22, 29, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 22, 22, 29, 29, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 174) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/174 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/174' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1) `ZINC001577824462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577824462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577824462 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 10, 14, 26, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 14, 14, 26, 26, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577824462 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 Building ZINC001577824462 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577824462 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 173) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1) `ZINC001577824462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577824462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577824462 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 12, 22, 29, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 12, 12, 22, 22, 29, 29, 50, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 174) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1) `ZINC001577824462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577824462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577824462 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCCNC(=O)c2ccc[nH]2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 7, 7, 7, 7, 10, 14, 26, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 10, 10, 14, 14, 26, 26, 50, 50, 50, 50, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577824462 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824462 Building ZINC001577824540 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577824540 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 175) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/175 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/175' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577824540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824540 none C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 33, 33, 16, 9, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 33, 16, 16, 9, 9, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 176) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/176 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/176' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577824540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824540 none C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 32, 32, 17, 9, 6, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 32, 17, 17, 9, 9, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577824540 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 Building ZINC001577824540 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577824540 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 175) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577824540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824540 none C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 33, 33, 16, 9, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 33, 16, 16, 9, 9, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 176) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577824540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824540 none C[C@@H]1C[C@@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 32, 32, 17, 9, 6, 4, 4, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 32, 17, 17, 9, 9, 6, 6, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577824540 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824540 Building ZINC001577824541 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577824541 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 177) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/177 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/177' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577824541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824541 none C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 33, 33, 16, 9, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 33, 16, 16, 9, 9, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 178) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/178 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/178' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577824541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824541 none C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 12, 7, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 34, 22, 22, 12, 12, 7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577824541 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 Building ZINC001577824541 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577824541 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 177) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577824541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824541 none C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 33, 33, 16, 9, 5, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50, 33, 16, 16, 9, 9, 5, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 178) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577824541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577824541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577824541 none C[C@H]1C[C@H]1C(=O)NCCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 34, 50, 34, 34, 22, 12, 7, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 34, 22, 22, 12, 12, 7, 7, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577824541 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577824541 Building ZINC001577848422 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577848422 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 179) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/179 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/179' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577848422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848422 none CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 27, 47, 47, 27, 27, 9, 7, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 47, 47, 47, 27, 9, 9, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 180) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/180 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/180' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577848422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848422 none CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 31, 47, 47, 31, 31, 12, 9, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 47, 47, 47, 31, 12, 12, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577848422 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 Building ZINC001577848422 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577848422 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 179) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848422.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577848422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848422 none CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 27, 47, 47, 27, 27, 9, 7, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 47, 47, 47, 27, 9, 9, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 180) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848422.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577848422.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848422 none CS[C@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 31, 47, 47, 31, 31, 12, 9, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 47, 47, 47, 31, 12, 12, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577848422 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848422 Building ZINC001577848423 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577848423 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 181) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/181 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/181' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577848423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848423 none CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 29, 48, 48, 29, 29, 9, 7, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 48, 48, 48, 29, 9, 9, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 182) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/182 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/182' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577848423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848423 none CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 48, 48, 25, 25, 12, 9, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 48, 48, 48, 25, 12, 12, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577848423 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 Building ZINC001577848423 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577848423 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 181) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848423.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577848423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848423 none CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 29, 48, 48, 29, 29, 9, 7, 4, 4, 4, 4, 3, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 48, 48, 48, 29, 9, 9, 7, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 182) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848423.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577848423.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577848423 none CS[C@@H](C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'S.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 14, 5, 7, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 25, 48, 48, 25, 25, 12, 9, 5, 5, 5, 5, 3, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 48, 48, 48, 25, 12, 12, 9, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577848423 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848423 Building ZINC001577848493 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577848493 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 183) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/183 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/183' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577848493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577848493 none CCCOCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 29, 10, 10, 10, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 29, 29, 10, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 184) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/184 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/184' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCOCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577848493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577848493 none CCCOCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 37, 16, 16, 16, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 37, 37, 16, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 45, 50, 49, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577848493 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 Building ZINC001577848493 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577848493 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 183) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCOCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577848493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577848493 none CCCOCC(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 40, 29, 10, 10, 10, 3, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 29, 29, 10, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 184) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCOCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577848493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577848493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001577848493 none CCCOCC(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 12, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 44, 37, 16, 16, 16, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50, 50, 50, 37, 37, 16, 4, 4, 4, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2] 50 rigid atoms, others: [48, 45, 50, 49, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52, 53, 54]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577848493 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577848493 Building ZINC001577850066 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850066 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 185) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/185 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/185' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850066 none Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 29, 39, 29, 29, 29, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 186) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/186 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/186' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850066 none Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 33, 43, 33, 33, 33, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850066 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 Building ZINC001577850066 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850066 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 185) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850066.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850066 none Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 29, 39, 29, 29, 29, 14, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 50, 50, 50, 50, 50, 29, 29, 29, 29, 12, 12, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 186) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850066.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850066.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850066 none Cc1[nH]ccc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 6, 1, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 43, 33, 43, 33, 33, 33, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850066 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850066 Building ZINC001577850130 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850130 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 187) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/187 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/187' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1) `ZINC001577850130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850130 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 1, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 17, 17, 27, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 12, 12, 12, 12, 27, 27, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 141 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 188) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/188 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/188' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1) `ZINC001577850130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850130 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 1, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 21, 21, 29, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 14, 14, 14, 14, 29, 29, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850130 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 Building ZINC001577850130 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850130 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 187) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1) `ZINC001577850130.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850130 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 1, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 12, 12, 12, 12, 17, 17, 27, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 12, 12, 12, 12, 27, 27, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 141 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 188) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1) `ZINC001577850130.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850130.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850130 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)Cc2ccoc2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 1, 1, 1, 12, 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, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 14, 14, 14, 14, 21, 21, 29, 50, 50, 50, 50, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 5, 5, 14, 14, 14, 14, 29, 29, 50, 50, 50, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 7, 5, 34, 25, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 138 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850130 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850130 Building ZINC001577850152 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850152 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 189) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/189 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/189' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1) `ZINC001577850152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001577850152 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 31, 31, 31, 31, 44, 47, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 151 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 190) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/190 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/190' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1) `ZINC001577850152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001577850152 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 31, 31, 31, 31, 46, 47, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850152 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 Building ZINC001577850152 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850152 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 189) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1) `ZINC001577850152.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001577850152 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 31, 31, 31, 31, 44, 47, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 151 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 190) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1) `ZINC001577850152.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850152.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 59 natoms 58 natoms 57 natoms 56 names: ZINC001577850152 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2C[C@H]3C[C@H]3C2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.3', 'C.3', '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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 7, 5, 5, 7, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 31, 31, 31, 31, 46, 47, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 13, 13, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55]) total number of confs: 156 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850152 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850152 Building ZINC001577850174 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850174 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 191) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/191 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/191' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850174 none Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 28, 47, 28, 28, 28, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 28, 28, 28, 28, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 192) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/192 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/192' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850174 none Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 28, 45, 28, 28, 28, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 28, 28, 28, 28, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850174 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 Building ZINC001577850174 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850174 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 191) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850174.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850174 none Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 28, 47, 28, 28, 28, 12, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 28, 28, 28, 28, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 192) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850174.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850174.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577850174 none Cc1c[nH]nc1C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 6, 8, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 28, 45, 28, 28, 28, 14, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 28, 50, 50, 50, 50, 28, 28, 28, 28, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850174 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850174 Building ZINC001577850329 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850329 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 193) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/193 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/193' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1) `ZINC001577850329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850329 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 17, 26, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 26, 26, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 194) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/194 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/194' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1) `ZINC001577850329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850329 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 14, 25, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 25, 25, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850329 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 Building ZINC001577850329 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850329 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 193) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1) `ZINC001577850329.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850329 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 8, 8, 8, 8, 17, 26, 50, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 17, 17, 26, 26, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 194) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1) `ZINC001577850329.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850329.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850329 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 14, 25, 50, 50, 50, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 25, 25, 50, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850329 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850329 Building ZINC001577850535 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850535 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 195) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/195 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/195' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1) `ZINC001577850535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850535 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 40, 40, 40, 40, 50, 50, 40, 40, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 196) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/196 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/196' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1) `ZINC001577850535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850535 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850535 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 Building ZINC001577850535 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850535 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 195) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1) `ZINC001577850535.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850535 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 40, 40, 40, 40, 50, 50, 50, 50, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 15, 15, 40, 40, 40, 40, 50, 50, 40, 40, 40, 40] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 196) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1) `ZINC001577850535.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850535.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577850535 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)c2cocn2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 12, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 37, 37, 37, 37, 50, 50, 50, 50, 50, 50, 37, 37, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 18, 37, 37, 37, 37, 50, 50, 37, 37, 37, 37] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850535 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850535 Building ZINC001577850628 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850628 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 197) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/197 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/197' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850628 none CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 32, 45, 32, 32, 32, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 32, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 198) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/198 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/198' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850628 none CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 50, 33, 46, 33, 33, 33, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850628 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 Building ZINC001577850628 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850628 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 197) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850628.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850628 none CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 32, 45, 32, 32, 32, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 50, 50, 50, 50, 50, 32, 32, 32, 32, 16, 16, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 198) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850628.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850628.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850628 none CC[C@@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 50, 33, 46, 33, 33, 33, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 33, 50, 50, 50, 50, 50, 33, 33, 33, 33, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 33, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 160 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850628 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850628 Building ZINC001577850630 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850630 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 199) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/199 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/199' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850630 none CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 34, 45, 34, 34, 34, 22, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 34, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 200) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/200 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/200' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850630 none CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 35, 44, 35, 35, 35, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850630 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 Building ZINC001577850630 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850630 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 199) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850630.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850630 none CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 45, 50, 50, 34, 45, 34, 34, 34, 22, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 50, 50, 50, 50, 50, 34, 34, 34, 34, 19, 19, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 169 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 200) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577850630.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850630.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577850630 none CC[C@H](F)C(=O)N1CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'F', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 15, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 50, 50, 35, 44, 35, 35, 35, 23, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 20, 20, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850630 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850630 Building ZINC001577850997 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850997 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 201) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/201 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/201' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1) `ZINC001577850997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850997 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 30, 30, 30, 30, 37, 37, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 202) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/202 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/202' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1) `ZINC001577850997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850997 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 31, 31, 31, 31, 38, 38, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 18, 18, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850997 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 Building ZINC001577850997 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850997 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 201) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1) `ZINC001577850997.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850997 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 19, 30, 30, 30, 30, 37, 37, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 16, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 161 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 202) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1) `ZINC001577850997.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850997.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850997 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 31, 31, 31, 31, 38, 38, 50, 50, 50, 50, 50, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 18, 18, 31, 31, 31, 31, 50, 50, 50, 50, 50, 50, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 168 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850997 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850997 Building ZINC001577850998 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850998 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 203) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/203 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/203' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1) `ZINC001577850998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850998 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 28, 28, 28, 28, 35, 35, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 204) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/204 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/204' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1) `ZINC001577850998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850998 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 30, 30, 30, 30, 38, 38, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850998 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 Building ZINC001577850998 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577850998 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 203) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/203: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1) `ZINC001577850998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577850998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850998 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 28, 28, 28, 28, 35, 35, 50, 50, 50, 50, 50, 28, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 16, 16, 28, 28, 28, 28, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 204) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/204: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1) `ZINC001577850998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577850998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577850998 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NCCN1CCN(C(=O)[C@@H]2CC23CC3)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 20, 30, 30, 30, 30, 38, 38, 50, 50, 50, 50, 50, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 17, 17, 30, 30, 30, 30, 50, 50, 50, 50, 50, 50, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577850998 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577850998 Building ZINC001577862067 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577862067 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 205) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/205 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/205' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577862067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577862067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577862067 none Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 20, 16, 7, 7, 7, 7, 6, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 42, 20, 20, 16, 16, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 206) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/206 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/206' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577862067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577862067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577862067 none Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 44, 44, 18, 15, 7, 7, 7, 7, 5, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 44, 18, 18, 15, 15, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577862067 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 Building ZINC001577862067 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577862067 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 205) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577862067.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577862067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577862067 none Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 20, 16, 7, 7, 7, 7, 6, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 42, 20, 20, 16, 16, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 206) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577862067.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577862067.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577862067 none Cc1n[nH]cc1C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 6, 1, 1, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 44, 44, 18, 15, 7, 7, 7, 7, 5, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 44, 18, 18, 15, 15, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577862067 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862067 Building ZINC001577862094 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577862094 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 207) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/207 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/207' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1) `ZINC001577862094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577862094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577862094 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 9, 9, 9, 9, 16, 25, 50, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 25, 25, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 208) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/208 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/208' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1) `ZINC001577862094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577862094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577862094 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 14, 23, 46, 46, 46, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 23, 23, 46, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577862094 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 Building ZINC001577862094 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577862094 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 207) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1) `ZINC001577862094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577862094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577862094 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 9, 9, 9, 9, 16, 25, 50, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 16, 16, 25, 25, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 195 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 208) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1) `ZINC001577862094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577862094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577862094 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CCN(CCNC(=O)c2cnco2)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 1, 1, 8, 1, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 14, 23, 46, 46, 46, 50, 50, 50, 50, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 23, 23, 46, 50, 50, 6, 6, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577862094 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577862094 Building ZINC001577867306 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577867306 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 209) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/209 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/209' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577867306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577867306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001577867306 none CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 50, 49, 49, 21, 15, 7, 7, 7, 7, 6, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 21, 21, 15, 15, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 210) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/210 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/210' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577867306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577867306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001577867306 none CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 17, 8, 8, 8, 8, 6, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 17, 17, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577867306 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 Building ZINC001577867306 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577867306 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 209) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/209: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577867306.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577867306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001577867306 none CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 50, 49, 49, 21, 15, 7, 7, 7, 7, 6, 1, 3, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 21, 21, 15, 15, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 210) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/210: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001577867306.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577867306.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001577867306 none CC(C)(C)C(=O)NCCN1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 1, 11, 8, 5, 5, 10, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 25, 17, 8, 8, 8, 8, 6, 1, 3, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 17, 17, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [48, 45, 49, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577867306 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577867306 Building ZINC001577900923 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577900923 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 211) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/211 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/211' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900923 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 42, 42, 42, 42, 30, 42, 14, 30, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 42, 42, 42, 42, 42, 42, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 212) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/212 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/212' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900923 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 29, 44, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 165 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577900923 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 Building ZINC001577900923 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577900923 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 211) grep: /scratch/xiaobo/167320/xcr-8058097.70/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(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900923.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900923 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 50, 42, 42, 42, 42, 30, 42, 14, 30, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 42, 42, 42, 42, 42, 42, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 212) grep: /scratch/xiaobo/167320/xcr-8058097.70/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(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900923.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577900923.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900923 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 29, 44, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 165 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577900923 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900923 Building ZINC001577900924 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577900924 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 213) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/213 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/213' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900924 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 27, 44, 15, 27, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 44, 44, 44, 44, 44, 44, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 214) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/214 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/214' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900924 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 30, 44, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 165 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577900924 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 Building ZINC001577900924 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577900924 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 213) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900924.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900924 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 27, 44, 15, 27, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 44, 44, 44, 44, 44, 44, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 159 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 214) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577900924.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577900924.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577900924 none CC(=O)N1CCC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 50, 44, 44, 44, 44, 30, 44, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 44, 44, 44, 44, 44, 44, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 165 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577900924 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577900924 Building ZINC001577901107 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901107 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 215) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/215 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/215' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1) `ZINC001577901107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901107 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 17, 17, 17, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 216) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/216 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/216' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1) `ZINC001577901107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901107 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 16, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901107 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 Building ZINC001577901107 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901107 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 215) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1) `ZINC001577901107.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901107 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 17, 17, 17, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 216) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1) `ZINC001577901107.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901107.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901107 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cc3n(n2)CCCO3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 16, 16, 16, 25, 25, 50, 50, 50, 50, 50, 50, 50, 50, 16, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 16, 16, 16, 16, 50, 50, 50, 50, 50, 50, 50, 16, 16] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 126 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901107 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901107 Building ZINC001577901258 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901258 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 217) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/217 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/217' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001577901258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577901258 none Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 14, 11, 14, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 218) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/218 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/218' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001577901258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577901258 none Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 38, 15, 11, 15, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 39, 39, 38, 38, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901258 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 Building ZINC001577901258 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901258 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 217) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001577901258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577901258 none Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 14, 11, 14, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 33, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 218) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001577901258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577901258 none Cc1c(CCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 39, 38, 15, 11, 15, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 39, 39, 38, 38, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901258 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901258 Building ZINC001577901291 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901291 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 219) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/219 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/219' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901291 none CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 22, 32, 32, 11, 22, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 203 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 220) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/220 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/220' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901291 none CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 22, 37, 37, 11, 22, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 209 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901291 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 Building ZINC001577901291 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901291 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 219) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901291.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901291 none CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 22, 32, 32, 11, 22, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 32, 32, 32, 32, 32, 32, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 203 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 220) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901291.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901291.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901291 none CC(=O)NC(C)(C)C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 22, 37, 37, 11, 22, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 37, 37, 37, 37, 37, 37, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 209 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901291 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901291 Building ZINC001577901294 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901294 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 221) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/221 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/221' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901294 none CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 16, 11, 16, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 222) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/222 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/222' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901294 none CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 15, 10, 15, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901294 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 Building ZINC001577901294 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901294 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 221) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901294.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901294 none CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 16, 11, 16, 11, 11, 11, 4, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 222) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901294.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901294.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901294 none CCCn1cc(C(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 15, 10, 15, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901294 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901294 Building ZINC001577901295 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901295 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 223) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/223 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/223' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901295 none CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 16, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 224) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/224 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/224' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901295 none CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 17, 15, 17, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901295 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 Building ZINC001577901295 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901295 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 223) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901295.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901295 none CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 16, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 224) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001577901295.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901295.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577901295 none CCCn1cc(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 17, 15, 17, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 15, 15, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901295 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901295 Building ZINC001577901352 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901352 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 225) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/225 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/225' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901352 none CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 25, 25, 19, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 25, 19, 19, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 226) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/226 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/226' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901352 none CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 24, 24, 18, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 24, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901352 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 Building ZINC001577901352 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901352 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 225) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901352.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901352 none CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 25, 25, 19, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 25, 19, 19, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 226) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901352.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901352.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901352 none CCCC(=O)NCC(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 24, 24, 24, 18, 13, 10, 13, 10, 10, 10, 4, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 24, 18, 18, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901352 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901352 Building ZINC001577901353 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901353 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 227) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/227 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/227' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901353 none CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 25, 25, 16, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 25, 16, 16, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 228) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/228 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/228' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901353 none CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 26, 26, 26, 17, 10, 9, 10, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 26, 17, 17, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901353 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 Building ZINC001577901353 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901353 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 227) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901353.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901353 none CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 25, 25, 25, 16, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 25, 16, 16, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 228) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577901353.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901353.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577901353 none CCCC(=O)NCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 26, 26, 26, 17, 10, 9, 10, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 26, 17, 17, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901353 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901353 Building ZINC001577901459 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901459 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 229) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/229 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/229' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901459 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 230) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/230 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/230' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901459 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 22, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901459 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 Building ZINC001577901459 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901459 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 229) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901459.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901459 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 145 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 230) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901459.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901459.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901459 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 22, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901459 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901459 Building ZINC001577901460 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901460 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 231) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/231 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/231' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901460 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 232) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/232 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/232' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901460 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901460 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 Building ZINC001577901460 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901460 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 231) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901460.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901460 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 21, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 232) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901460.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901460.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901460 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 26, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901460 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901460 Building ZINC001577901461 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901461 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 233) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/233 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/233' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901461 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 234) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/234 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/234' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901461 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901461 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 Building ZINC001577901461 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901461 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 233) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901461.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901461 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 234) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901461.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901461.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901461 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)[C@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 25, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 143 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901461 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901461 Building ZINC001577901462 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901462 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 235) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/235 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/235' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901462 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 236) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/236 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/236' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901462 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901462 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 Building ZINC001577901462 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901462 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 235) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901462.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901462 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 26, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 236) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1) `ZINC001577901462.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901462.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577901462 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@H]2CCc3n[nH]cc3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 1, 8, 8, 6, 1, 1, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 23, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 50, 50, 50, 50, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 148 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901462 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901462 Building ZINC001577901635 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901635 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 237) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/237 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/237' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1) `ZINC001577901635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577901635 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 238) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/238 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/238' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1) `ZINC001577901635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577901635 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901635 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 Building ZINC001577901635 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901635 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 237) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1) `ZINC001577901635.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577901635 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 124 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 238) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1) `ZINC001577901635.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901635.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577901635 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2nccn3ccnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 1, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 14, 14, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 122 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901635 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901635 Building ZINC001577901705 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901705 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 239) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/239 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/239' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1) `ZINC001577901705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577901705 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 17, 17, 40, 42, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 40, 40, 42, 42, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 240) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/240 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/240' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1) `ZINC001577901705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577901705 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 17, 17, 38, 41, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 38, 38, 41, 41, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901705 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 Building ZINC001577901705 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901705 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 239) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1) `ZINC001577901705.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577901705 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 17, 17, 40, 42, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 40, 40, 42, 42, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 240) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1) `ZINC001577901705.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901705.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577901705 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 17, 17, 38, 41, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 38, 38, 41, 41, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901705 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901705 Building ZINC001577901721 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901721 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 241) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/241 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/241' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1) `ZINC001577901721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901721 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 17, 17, 17, 17, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 242) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/242 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/242' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1) `ZINC001577901721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901721 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 17, 17, 17, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901721 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 Building ZINC001577901721 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577901721 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 241) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/241: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1) `ZINC001577901721.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577901721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901721 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 17, 17, 17, 17, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 116 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 242) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/242: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1) `ZINC001577901721.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577901721.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001577901721 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 17, 17, 17, 17, 17, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577901721 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577901721 Building ZINC001577904232 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904232 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 243) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/243 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/243' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577904232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904232 none Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 33, 33, 33, 13, 33, 10, 13, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 33, 33, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 244) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/244 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/244' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577904232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904232 none Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 35, 35, 35, 16, 35, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 35, 35, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904232 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 Building ZINC001577904232 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904232 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 243) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577904232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904232 none Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 33, 33, 33, 13, 33, 10, 13, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 33, 33, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 244) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577904232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904232 none Cn1cc([C@@H]2C[C@H]2C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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, 8, 1, 1, 5, 7, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 35, 35, 35, 35, 16, 35, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 35, 35, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 125 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904232 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904232 Building ZINC001577904373 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904373 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 245) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/245 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/245' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904373 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 17, 17, 17, 17, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 246) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/246 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/246' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904373 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 19, 19, 19, 19, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904373 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 Building ZINC001577904373 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904373 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 245) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904373 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 17, 17, 17, 17, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 246) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904373 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 19, 19, 19, 19, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 19, 19, 19, 19, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904373 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904373 Building ZINC001577904374 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904374 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 247) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/247 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/247' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904374 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 248) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/248 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/248' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904374 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 21, 21, 21, 21, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904374 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 Building ZINC001577904374 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904374 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 247) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904374.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904374 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 248) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1) `ZINC001577904374.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904374.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001577904374 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3nccn3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 21, 21, 21, 21, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 21, 21, 21, 21, 50, 50, 50, 50, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904374 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904374 Building ZINC001577904407 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904407 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 249) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/249 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/249' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 250) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/250 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/250' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 251) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/251 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/251' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 252) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/252 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/252' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904407 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 Building ZINC001577904407 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904407 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 249) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 250) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 251) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 252) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904407 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 Building ZINC001577904407 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904407 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 249) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 250) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 251) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 252) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904407 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 Building ZINC001577904407 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904407 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 249) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 250) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 159 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 251) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/251: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 252) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/252: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904407.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904407.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904407 none CCN1CCOC[C@@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 17, 35, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 155 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904407 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904407 Building ZINC001577904408 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904408 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 253) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/253 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/253' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 254) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/254 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/254' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 255) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/255 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/255' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 256) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/256 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/256' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904408 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 Building ZINC001577904408 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904408 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 253) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 254) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 255) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 256) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904408 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 Building ZINC001577904408 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904408 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 253) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 254) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 255) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 256) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904408 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 Building ZINC001577904408 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904408 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 253) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 254) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 50, 17, 32, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 255) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/255: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 256) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/256: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904408.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904408 none CCN1CCOC[C@H]1C(=O)N1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 16, 31, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904408 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904408 Building ZINC001577904409 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904409 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 257) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/257 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/257' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 258) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/258 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/258' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 259) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/259 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/259' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 260) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/260 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/260' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904409 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 Building ZINC001577904409 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904409 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 257) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 258) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 259) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 260) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904409 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 Building ZINC001577904409 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904409 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 257) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 258) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 259) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 260) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904409 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 Building ZINC001577904409 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904409 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 257) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 258) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 50, 18, 38, 18, 18, 18, 4, 18, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 18, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 18] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 259) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/259: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 260) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/260: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904409.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904409 none CCN1CCOC[C@@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 17, 37, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 153 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904409 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904409 Building ZINC001577904410 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904410 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 261) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/261 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/261' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 262) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/262 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/262' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 263) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/263 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/263' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 264) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/264 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/264' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904410 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 Building ZINC001577904410 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904410 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 261) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 262) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 263) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 264) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904410 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 Building ZINC001577904410 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904410 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 261) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 262) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 263) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 264) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904410 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 Building ZINC001577904410 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001577904410 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 261) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 262) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 29, 50, 14, 29, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 40 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 263) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/263: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 264) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/264: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904410.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001577904410.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001577904410 none CCN1CCOC[C@H]1C(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 50, 16, 30, 16, 16, 16, 4, 16, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 16, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 149 number of broken/clashed sets: 41 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904410 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904410 Building ZINC001577904475 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904475 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 265) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/265 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/265' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904475 none CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 42, 24, 9, 7, 9, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 49, 49, 24, 24, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 266) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/266 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/266' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904475 none CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 26, 10, 8, 10, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904475 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 Building ZINC001577904475 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904475 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 265) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904475.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904475 none CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 42, 24, 9, 7, 9, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 49, 49, 24, 24, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 266) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577904475.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904475.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577904475 none CCOCCOCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 26, 10, 8, 10, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904475 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904475 Building ZINC001577904645 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904645 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 267) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/267 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/267' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001577904645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577904645 none Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 9, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 33, 33, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 268) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/268 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/268' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001577904645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577904645 none Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 9, 7, 9, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 30, 30, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904645 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 Building ZINC001577904645 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904645 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 267) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/267: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001577904645.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577904645 none Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 9, 8, 9, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 33, 33, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 268) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/268: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001577904645.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904645.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001577904645 none Cc1cc(OCC(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 12, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 30, 9, 7, 9, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 30, 30, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 14, 15, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001577904645 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904645 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904645 Building ZINC001577904677 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904677 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 269) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/269 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/269' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001577904677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904677 none CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 18, 7, 5, 7, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 34, 50, 50, 50, 50, 50, 34, 34, 18, 18, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 270) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/270 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/270' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001577904677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904677 none CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 20, 10, 7, 10, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 50, 50, 50, 50, 50, 34, 34, 20, 20, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904677 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 Building ZINC001577904677 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904677 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 269) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001577904677.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904677 none CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 18, 7, 5, 7, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 34, 50, 50, 50, 50, 50, 34, 34, 18, 18, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 270) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001577904677.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904677.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904677 none CCn1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 34, 20, 10, 7, 10, 7, 7, 7, 2, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 34, 50, 50, 50, 50, 50, 34, 34, 20, 20, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 48, 49]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904677 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904677 Building ZINC001577904695 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904695 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 271) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/271 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/271' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1) `ZINC001577904695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904695 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 13, 13, 25, 43, 48, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 272) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/272 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/272' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1) `ZINC001577904695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904695 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 13, 13, 27, 41, 47, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 27, 27, 47, 47, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904695 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 Building ZINC001577904695 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904695 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 271) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1) `ZINC001577904695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904695 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 13, 13, 25, 43, 48, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 25, 25, 47, 47, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 272) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1) `ZINC001577904695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904695 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 13, 13, 27, 41, 47, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 27, 27, 47, 47, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904695 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904695 Building ZINC001577904696 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904696 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 273) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/273 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/273' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1) `ZINC001577904696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904696 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 10, 10, 24, 38, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 274) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/274 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/274' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1) `ZINC001577904696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904696 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 12, 12, 25, 38, 49, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 25, 25, 48, 48, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904696 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 Building ZINC001577904696 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904696 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 273) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1) `ZINC001577904696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904696 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 10, 10, 24, 38, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 24, 24, 47, 47, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 274) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1) `ZINC001577904696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001577904696 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)COC[C@@H]2CCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 12, 12, 25, 38, 49, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 11, 11, 25, 25, 48, 48, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904696 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904696 Building ZINC001577904724 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904724 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 275) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/275 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/275' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001577904724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904724 none COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 38, 38, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 276) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/276 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/276' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001577904724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904724 none COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 8, 5, 8, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 36, 36, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904724 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 Building ZINC001577904724 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904724 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 275) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001577904724.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904724 none COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 10, 8, 10, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 38, 38, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 276) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1) `ZINC001577904724.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904724.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577904724 none COc1ccc(CC(=O)N2CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 36, 8, 5, 8, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 36, 36, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 47, 48, 49]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904724 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904724 Building ZINC001577904881 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904881 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 277) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/277 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/277' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904881 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 22, 22, 22, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 278) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/278 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/278' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904881 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 23, 23, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904881 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 Building ZINC001577904881 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904881 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 277) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/277: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904881.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904881 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 18, 18, 22, 22, 22, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 22, 22, 22, 22, 50, 50, 50, 50, 50, 50, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 278) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/278: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904881.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904881.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904881 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 23, 23, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904881 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904881 Building ZINC001577904882 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904882 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 279) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/279 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/279' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904882 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 23, 23, 23, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 280) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/280 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/280' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904882 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 25, 25, 25, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904882 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 Building ZINC001577904882 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577904882 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 279) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904882.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577904882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904882 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 23, 23, 23, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 280) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1) `ZINC001577904882.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577904882.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577904882 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1CCN(C(=O)c2noc3c2COCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'O.3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 12, 1, 1, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 19, 19, 25, 25, 25, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 25, 25, 25, 25, 50, 50, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577904882 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577904882 Building ZINC001577919650 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577919650 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 281) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/281 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/281' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1) `ZINC001577919650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577919650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001577919650 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 31, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 45, 45, 48, 48, 48, 48, 48, 45, 45, 46, 46, 46, 46, 46, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 282) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/282 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/282' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1) `ZINC001577919650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577919650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001577919650 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 30, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 44, 44, 44, 44, 47, 47, 47, 47, 47, 44, 44, 45, 45, 45, 45, 45, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577919650 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 Building ZINC001577919650 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577919650 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 281) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1) `ZINC001577919650.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577919650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001577919650 none CCN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [46, 31, 17, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 45, 45, 45, 45, 48, 48, 48, 48, 48, 45, 45, 46, 46, 46, 46, 46, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 45] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 221 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 282) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1) `ZINC001577919650.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577919650.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001577919650 none CCN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnc(c2nn[nH]n2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.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'] dock atom type numbers: [5, 5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [45, 30, 16, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 44, 44, 44, 44, 47, 47, 47, 47, 47, 44, 44, 45, 45, 45, 45, 45, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 215 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577919650 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577919650 Building ZINC001577944748 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577944748 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 283) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/283 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/283' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577944748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577944748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577944748 none CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 40, 33, 23, 9, 9, 9, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 49, 49, 40, 40, 23, 23, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 284) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/284 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/284' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577944748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577944748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577944748 none CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 36, 26, 16, 7, 7, 7, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 49, 49, 36, 36, 16, 16, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577944748 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 Building ZINC001577944748 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577944748 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 283) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577944748.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577944748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577944748 none CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 40, 33, 23, 9, 9, 9, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 49, 49, 40, 40, 23, 23, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 284) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001577944748.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577944748.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001577944748 none CCOCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 12, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 36, 26, 16, 7, 7, 7, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 49, 49, 36, 36, 16, 16, 7, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577944748 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944748 Building ZINC001577944770 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577944770 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 285) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/285 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/285' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577944770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577944770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577944770 none Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 35, 9, 9, 9, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 37, 37, 35, 35, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 286) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/286 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/286' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577944770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577944770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577944770 none Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 32, 11, 11, 11, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 34, 34, 32, 32, 11, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577944770 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 Building ZINC001577944770 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577944770 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 285) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577944770.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577944770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577944770 none Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 37, 35, 9, 9, 9, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 37, 37, 35, 35, 9, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 286) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001577944770.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577944770.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001577944770 none Cn1cc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 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, 32, 11, 11, 11, 6, 6, 6, 6, 6, 3, 1, 5, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 34, 34, 32, 32, 11, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577944770 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577944770 Building ZINC001577971877 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577971877 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 287) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/287 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/287' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577971877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971877 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 15, 15, 15, 46, 50, 50, 50, 49, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 46, 46, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 288) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/288 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/288' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577971877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971877 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 16, 16, 16, 46, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 46, 46, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577971877 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 Building ZINC001577971877 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577971877 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 287) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971877.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577971877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971877 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 15, 15, 15, 46, 50, 50, 50, 49, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 15, 46, 46, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 288) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971877.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577971877.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971877 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 16, 16, 16, 46, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 46, 46, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577971877 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971877 Building ZINC001577971878 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577971878 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 289) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/289 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/289' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577971878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971878 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 44, 44, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 290) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/290 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/290' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577971878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971878 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 16, 16, 16, 48, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 48, 48, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577971878 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 Building ZINC001577971878 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001577971878 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 289) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971878.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001577971878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971878 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 44, 44, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 290) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1) `ZINC001577971878.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001577971878.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001577971878 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 5, 6, 6, 6, 6, 6, 16, 16, 16, 48, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 16, 48, 48, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001577971878 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001577971878 Building ZINC001578031667 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578031667 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 291) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/291 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/291' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1) `ZINC001578031667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578031667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578031667 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 8, 8, 8, 18, 24, 40, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 18, 18, 40, 40, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 292) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/292 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/292' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1) `ZINC001578031667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578031667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578031667 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 10, 10, 10, 21, 25, 42, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 21, 21, 42, 42, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578031667 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 Building ZINC001578031667 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578031667 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 291) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1) `ZINC001578031667.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578031667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578031667 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 8, 8, 8, 18, 24, 40, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 8, 18, 18, 40, 40, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 292) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1) `ZINC001578031667.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578031667.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578031667 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](NC(=O)COCc2cccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 1, 1, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 10, 10, 10, 21, 25, 42, 50, 50, 50, 50, 50, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 10, 21, 21, 42, 42, 50, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578031667 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578031667 Building ZINC001578032366 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578032366 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 293) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/293 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/293' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578032366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578032366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578032366 none CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 23, 50, 23, 23, 10, 10, 10, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 294) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/294 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/294' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578032366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578032366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578032366 none CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 22, 49, 22, 22, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578032366 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 Building ZINC001578032366 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578032366 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 293) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578032366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578032366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578032366 none CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 23, 50, 23, 23, 10, 10, 10, 10, 10, 4, 1, 6, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 10, 10, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 246 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 294) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578032366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578032366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578032366 none CC(C)[C@@H](C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 49, 50, 22, 49, 22, 22, 9, 9, 9, 9, 9, 4, 1, 7, 1, 1, 1, 1, 1, 1, 9, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 266 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578032366 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578032366 Building ZINC001578059749 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578059749 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 295) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/295 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/295' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1) `ZINC001578059749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578059749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578059749 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 17, 17, 17, 44, 50, 50, 50, 48, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 44, 44, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 296) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/296 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/296' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1) `ZINC001578059749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578059749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578059749 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 20, 20, 20, 44, 50, 50, 50, 49, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 44, 44, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578059749 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 Building ZINC001578059749 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578059749 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 295) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/295: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1) `ZINC001578059749.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578059749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578059749 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 17, 17, 17, 44, 50, 50, 50, 48, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 17, 44, 44, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 296) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/296: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1) `ZINC001578059749.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578059749.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578059749 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCc2ncccn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 1, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 6, 8, 8, 8, 8, 8, 20, 20, 20, 44, 50, 50, 50, 49, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 20, 44, 44, 50, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578059749 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578059749 Building ZINC001578064297 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578064297 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 297) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/297 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/297' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578064297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064297 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 12, 31, 31, 39, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 31, 31, 31, 39, 39, 50, 50, 50, 50, 50, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 298) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/298 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/298' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578064297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064297 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 28, 28, 36, 50, 50, 50, 50, 50, 10, 10, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 28, 28, 28, 36, 36, 50, 50, 50, 50, 50, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578064297 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 Building ZINC001578064297 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578064297 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 297) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064297.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578064297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064297 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 12, 31, 31, 39, 50, 50, 50, 50, 50, 12, 12, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 31, 31, 31, 39, 39, 50, 50, 50, 50, 50, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 298) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064297.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578064297.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064297 none C[C@@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 10, 28, 28, 36, 50, 50, 50, 50, 50, 10, 10, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 28, 28, 28, 36, 36, 50, 50, 50, 50, 50, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578064297 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064297 Building ZINC001578064298 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578064298 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 299) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/299 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/299' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578064298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064298 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 12, 32, 32, 42, 50, 50, 50, 50, 50, 12, 12, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 32, 32, 32, 42, 42, 50, 50, 50, 50, 50, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 300) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/300 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/300' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578064298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064298 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 32, 37, 50, 50, 50, 50, 50, 18, 18, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 37, 37, 50, 50, 50, 50, 50, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578064298 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 Building ZINC001578064298 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578064298 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 299) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064298.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578064298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064298 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 12, 32, 32, 42, 50, 50, 50, 50, 50, 12, 12, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 32, 32, 32, 42, 42, 50, 50, 50, 50, 50, 12, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 300) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578064298.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578064298.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578064298 none C[C@H](Cc1cnn(C)c1)C(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 1, 8, 8, 5, 1, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 32, 37, 50, 50, 50, 50, 50, 18, 18, 7, 7, 7, 7, 7, 3, 1, 6, 1, 1, 1, 1, 1, 1, 7, 32, 32, 32, 37, 37, 50, 50, 50, 50, 50, 18, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578064298 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578064298 Building ZINC001578070557 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578070557 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 301) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/301 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/301' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578070557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070557 none COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 28, 18, 9, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 38, 38, 28, 28, 9, 9, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 302) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/302 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/302' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578070557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070557 none COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 30, 24, 16, 8, 8, 8, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 38, 38, 30, 30, 16, 16, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578070557 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 Building ZINC001578070557 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578070557 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 301) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070557.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578070557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070557 none COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 28, 18, 9, 4, 4, 4, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 38, 38, 28, 28, 9, 9, 4, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 302) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070557.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578070557.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070557 none COCCCOCC(=O)N[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 30, 24, 16, 8, 8, 8, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 38, 38, 30, 30, 16, 16, 8, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578070557 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070557 Building ZINC001578070558 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578070558 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 303) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/303 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/303' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578070558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070558 none COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 23, 17, 9, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 32, 32, 23, 23, 9, 9, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 304) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/304 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/304' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578070558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070558 none COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 25, 20, 12, 5, 5, 5, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 38, 38, 25, 25, 12, 12, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578070558 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 Building ZINC001578070558 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578070558 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 303) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070558.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578070558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070558 none COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 23, 17, 9, 4, 4, 4, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 32, 32, 23, 23, 9, 9, 4, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 304) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578070558.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578070558.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578070558 none COCCCOCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 5, 12, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 25, 20, 12, 5, 5, 5, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 38, 38, 25, 25, 12, 12, 5, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 217 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578070558 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578070558 Building ZINC001578125655 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125655 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 305) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/305 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/305' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 17, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 306) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/306 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/306' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 307) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/307 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/307' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 18, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 308) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/308 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/308' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125655 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 Building ZINC001578125655 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125655 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 305) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 17, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 306) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 307) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 18, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 308) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125655 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 Building ZINC001578125655 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125655 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 305) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 17, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 306) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 307) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 18, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 308) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125655 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 Building ZINC001578125655 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125655 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 305) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 17, 17, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 17, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 306) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 307) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/307: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 18, 18, 20, 20, 29, 50, 50, 50, 50, 50, 50, 50, 18, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 308) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/308: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125655.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125655.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125655 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 23, 23, 31, 50, 50, 50, 50, 50, 50, 50, 20, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 183 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125655 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125655 Building ZINC001578125656 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125656 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 309) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/309 `/scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 310) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/310 `/scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 311) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/311 `/scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 312) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/312 `/scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125656 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 Building ZINC001578125656 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125656 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 309) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 310) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 311) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 312) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125656 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 Building ZINC001578125656 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125656 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 309) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 310) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 311) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 312) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125656 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 Building ZINC001578125656 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578125656 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 309) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 310) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 311) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 19, 19, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 312) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1) `ZINC001578125656.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578125656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 58 natoms 57 natoms 56 natoms 55 names: ZINC001578125656 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)[C@H]1CC[N@@](C)CC1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 21, 21, 29, 29, 36, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 21, 21] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125656 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125656 Building ZINC001578125857 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578125857 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 313) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/313 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/313' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125857 none Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 21, 21, 21, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 44, 44, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 314) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/314 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/314' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125857 none Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 18, 18, 18, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 42, 42, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125857 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 Building ZINC001578125857 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578125857 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 313) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125857.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125857 none Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 21, 21, 21, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 44, 44, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 314) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125857.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125857.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125857 none Cn1ccc(CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 18, 18, 18, 11, 7, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 50, 50, 50, 50, 50, 50, 42, 42, 18, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125857 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125857 Building ZINC001578125859 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578125859 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 315) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/315 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/315' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125859 none Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 18, 18, 18, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 50, 50, 50, 50, 50, 50, 45, 45, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 316) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/316 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/316' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125859 none Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 16, 16, 16, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 50, 50, 50, 50, 50, 50, 43, 43, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125859 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 Building ZINC001578125859 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578125859 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 315) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125859.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578125859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125859 none Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 18, 18, 18, 10, 6, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 13, 13, 50, 50, 50, 50, 50, 50, 45, 45, 18, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 13, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 43, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 45, 46, 47, 48, 49]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 316) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578125859.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578125859.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578125859 none Cn1ccc(CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 16, 16, 16, 11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 50, 50, 50, 50, 50, 50, 43, 43, 16, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578125859 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578125859 Building ZINC001578126082 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126082 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 317) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/317 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/317' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126082 none COc1cnc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 50, 50, 41, 41, 41, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 30, 30, 50, 50, 50, 50, 50, 50, 41, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 318) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/318 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/318' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126082 none COc1cnc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 48, 48, 44, 44, 44, 24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 28, 28, 48, 48, 50, 50, 50, 48, 44, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 48] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126082 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 Building ZINC001578126082 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126082 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 317) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126082 none COc1cnc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 50, 50, 41, 41, 41, 27, 13, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 30, 30, 50, 50, 50, 50, 50, 50, 41, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 227 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 318) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126082 none COc1cnc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 48, 48, 44, 44, 44, 24, 10, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 28, 28, 48, 48, 50, 50, 50, 48, 44, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28, 28, 28, 28, 48] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 220 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126082 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126082 Building ZINC001578126083 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126083 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 319) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/319 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/319' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126083 none COc1cnc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 49, 49, 42, 42, 42, 27, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 29, 29, 49, 49, 49, 49, 49, 49, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 225 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 320) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/320 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/320' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126083 none COc1cnc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 50, 50, 40, 40, 40, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 32, 32, 50, 50, 50, 50, 50, 50, 40, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126083 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 Building ZINC001578126083 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126083 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 319) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126083 none COc1cnc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 42, 42, 49, 49, 42, 42, 42, 27, 11, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 29, 29, 49, 49, 49, 49, 49, 49, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 225 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 320) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578126083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126083 none COc1cnc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.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, 8, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 50, 50, 40, 40, 40, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 32, 32, 50, 50, 50, 50, 50, 50, 40, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 252 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126083 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126083 Building ZINC001578126316 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126316 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 321) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/321 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/321' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126316 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 28, 28, 28, 49, 49, 49, 49, 49, 49, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 322) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/322 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/322' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126316 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 25, 25, 25, 50, 50, 50, 50, 50, 50, 18, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126316 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 Building ZINC001578126316 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126316 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 321) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126316.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126316 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 22, 22, 28, 28, 28, 49, 49, 49, 49, 49, 49, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 28, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 322) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126316.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126316.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126316 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 25, 25, 25, 50, 50, 50, 50, 50, 50, 18, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 25, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126316 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126316 Building ZINC001578126317 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126317 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 323) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/323 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/323' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126317 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 24, 24, 24, 48, 48, 48, 48, 48, 48, 16, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 324) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/324 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/324' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126317 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 24, 24, 24, 48, 48, 48, 48, 48, 48, 20, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126317 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 Building ZINC001578126317 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126317 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 323) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126317 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 16, 16, 24, 24, 24, 48, 48, 48, 48, 48, 48, 16, 18, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 18, 18, 18, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 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/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 324) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578126317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578126317 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 12, 20, 20, 24, 24, 24, 48, 48, 48, 48, 48, 48, 20, 22, 22, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 22, 22, 22, 22, 22] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126317 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126317 Building ZINC001578126390 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126390 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 325) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/325 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/325' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126390 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 43, 43, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 43, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 326) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/326 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/326' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126390 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 40, 25, 10, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126390 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 Building ZINC001578126390 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126390 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 325) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126390 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 43, 43, 29, 13, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 43, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 191 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 326) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126390 none Cn1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 40, 25, 10, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 40, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126390 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126390 Building ZINC001578126391 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126391 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 327) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/327 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/327' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126391 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 41, 41, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 41, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 328) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/328 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/328' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126391 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 42, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126391 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 Building ZINC001578126391 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126391 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 327) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126391 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 41, 41, 26, 11, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 41, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 26, 26, 26, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 328) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O) `ZINC001578126391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001578126391 none Cn1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)ncc1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 1, 11, 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, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 42, 42, 28, 12, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 42, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 11, 13, 14, 15, 16, 17, 18] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126391 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126391 Building ZINC001578126408 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126408 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 329) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/329 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/329' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126408 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 26, 26, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 26, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 37, 50, 50, 37, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 330) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/330 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/330' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126408 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 39, 39, 39, 40, 40, 40, 50, 50, 40, 40, 29, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 39, 40, 50, 50, 40, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126408 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 Building ZINC001578126408 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126408 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 329) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126408.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126408 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 26, 26, 37, 37, 37, 37, 37, 37, 50, 50, 37, 37, 26, 27, 27, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 37, 37, 50, 50, 37, 27, 27, 27, 27, 27] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 330) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126408.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126408.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126408 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 11, 29, 29, 39, 39, 39, 40, 40, 40, 50, 50, 40, 40, 29, 30, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 39, 40, 50, 50, 40, 30, 30, 30, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126408 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126408 Building ZINC001578126409 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126409 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 331) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/331 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/331' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126409 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 28, 28, 39, 39, 39, 41, 41, 41, 50, 50, 41, 41, 26, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 41, 50, 50, 41, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 332) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/332 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/332' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126409 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 26, 26, 36, 36, 36, 37, 37, 37, 50, 50, 37, 37, 24, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 37, 50, 50, 37, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126409 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 Building ZINC001578126409 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126409 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 331) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/331: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126409.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126409 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 28, 28, 39, 39, 39, 41, 41, 41, 50, 50, 41, 41, 26, 29, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 39, 41, 50, 50, 41, 29, 29, 29, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 332) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/332: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1) `ZINC001578126409.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126409.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578126409 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)c1cc(C(N)=O)co1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 26, 26, 36, 36, 36, 37, 37, 37, 50, 50, 37, 37, 24, 31, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 36, 37, 50, 50, 37, 31, 31, 31, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126409 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126409 Building ZINC001578126504 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126504 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 333) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/333 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/333' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126504 none COc1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 35, 35, 35, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 23, 49, 49, 49, 49, 49, 49, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 334) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/334 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/334' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126504 none COc1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 38, 38, 38, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 31, 31, 48, 48, 50, 50, 50, 48, 38, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126504 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 Building ZINC001578126504 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126504 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 333) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126504.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126504 none COc1cc(C(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 35, 35, 35, 19, 10, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 23, 23, 49, 49, 49, 49, 49, 49, 35, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 23, 23, 23] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 334) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126504.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126504.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126504 none COc1cc(C(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 48, 48, 38, 38, 38, 25, 11, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 31, 31, 48, 48, 50, 50, 50, 48, 38, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31, 31, 31, 31] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126504 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126504 Building ZINC001578126505 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126505 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 335) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/335 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/335' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126505 none COc1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 39, 39, 39, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 29, 29, 49, 49, 49, 49, 49, 49, 39, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 336) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/336 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/336' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126505 none COc1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 48, 48, 32, 32, 32, 18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 48, 48, 49, 49, 49, 48, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126505 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 Building ZINC001578126505 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126505 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 335) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126505.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126505 none COc1cc(C(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 39, 39, 39, 28, 13, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 29, 29, 49, 49, 49, 49, 49, 49, 39, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 336) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1) `ZINC001578126505.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126505.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578126505 none COc1cc(C(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)on1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 12, 8, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 48, 48, 48, 32, 32, 32, 18, 10, 18, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 48, 48, 49, 49, 49, 48, 32, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22, 22, 22, 22] 50 rigid atoms, others: [33, 34, 35, 36, 37, 38, 39, 40, 41, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126505 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126505 Building ZINC001578126576 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126576 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 337) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/337 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/337' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126576 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 31, 31, 31, 36, 36, 50, 50, 50, 50, 50, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 31, 36, 36, 36, 36, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 338) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/338 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/338' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126576 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 31, 31, 31, 38, 38, 50, 50, 50, 50, 50, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 31, 38, 38, 38, 38, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126576 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 Building ZINC001578126576 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126576 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 337) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/337: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126576.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126576 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 22, 22, 31, 31, 31, 36, 36, 50, 50, 50, 50, 50, 22, 23, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 31, 36, 36, 36, 36, 50, 23, 23, 23, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 184 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 338) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/338: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126576.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126576.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126576 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 31, 31, 31, 38, 38, 50, 50, 50, 50, 50, 24, 24, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 31, 38, 38, 38, 38, 50, 24, 24, 24, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126576 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126576 Building ZINC001578126577 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126577 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 339) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/339 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/339' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126577 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 22, 22, 22, 35, 36, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 35, 35, 36, 36, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 340) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/340 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/340' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126577 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 24, 24, 24, 35, 35, 50, 50, 50, 50, 50, 18, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 35, 35, 35, 35, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126577 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 Building ZINC001578126577 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126577 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 339) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126577.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126577 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 17, 17, 22, 22, 22, 35, 36, 50, 50, 50, 50, 50, 17, 17, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 35, 35, 36, 36, 50, 17, 17, 17, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 340) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1) `ZINC001578126577.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126577.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578126577 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H](NC(=O)CCc1nc[nH]n1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 5, 1, 8, 1, 8, 6, 8, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 10, 18, 18, 24, 24, 24, 35, 35, 50, 50, 50, 50, 50, 18, 19, 19, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 35, 35, 35, 35, 50, 19, 19, 19, 19, 19] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 188 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126577 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126577 Building ZINC001578126578 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126578 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 341) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/341 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/341' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126578 none CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 50, 21, 21, 21, 15, 12, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 46, 46, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 342) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/342 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/342' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126578 none CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 24, 24, 24, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 50, 50, 50, 50, 50, 50, 47, 47, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126578 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 Building ZINC001578126578 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126578 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 341) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126578.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126578 none CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 50, 21, 21, 21, 15, 12, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 15, 15, 50, 50, 50, 50, 50, 50, 46, 46, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 208 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 342) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126578.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126578.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126578 none CN(C)C(=O)CC(=O)N[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 24, 24, 24, 13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 14, 14, 50, 50, 50, 50, 50, 50, 47, 47, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 14, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 198 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126578 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126578 Building ZINC001578126579 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126579 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 343) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/343 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/343' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126579 none CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 22, 22, 22, 12, 8, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 50, 50, 50, 50, 50, 50, 47, 47, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 344) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/344 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/344' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126579 none CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 50, 22, 22, 22, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 17, 17, 50, 50, 50, 50, 50, 50, 46, 46, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126579 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 Building ZINC001578126579 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578126579 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 343) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126579.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578126579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126579 none CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 50, 22, 22, 22, 12, 8, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 50, 50, 50, 50, 50, 50, 47, 47, 22, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 226 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 344) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578126579.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578126579.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578126579 none CN(C)C(=O)CC(=O)N[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 50, 22, 22, 22, 15, 10, 15, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 17, 17, 50, 50, 50, 50, 50, 50, 46, 46, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 217 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578126579 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578126579 Building ZINC001578133045 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578133045 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 345) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/345 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/345' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578133045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133045 none CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 26, 36, 16, 16, 16, 11, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 36, 26, 26, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 346) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/346 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/346' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578133045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133045 none CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 28, 32, 17, 17, 17, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 32, 28, 28, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578133045 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 Building ZINC001578133045 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578133045 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 345) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133045.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578133045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133045 none CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 26, 36, 16, 16, 16, 11, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 36, 26, 26, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 346) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133045.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578133045.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133045 none CCNC(=O)CC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 28, 32, 17, 17, 17, 11, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 50, 50, 50, 50, 50, 32, 28, 28, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 251 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578133045 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133045 Building ZINC001578133046 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578133046 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 347) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/347 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/347' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578133046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133046 none CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 26, 33, 15, 15, 15, 9, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 33, 26, 26, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 348) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/348 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/348' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578133046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133046 none CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 25, 36, 14, 14, 14, 9, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 36, 25, 25, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578133046 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 Building ZINC001578133046 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578133046 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 347) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133046.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578133046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133046 none CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 26, 33, 15, 15, 15, 9, 5, 2, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 6, 6, 50, 50, 50, 50, 50, 33, 26, 26, 15, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 249 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 348) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578133046.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578133046.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578133046 none CCNC(=O)CC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 36, 36, 25, 36, 14, 14, 14, 9, 4, 2, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 36, 25, 25, 14, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 241 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578133046 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578133046 Building ZINC001578148010 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578148010 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 349) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/349 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/349' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578148010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148010 none COc1cncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 48, 48, 48, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 49, 49, 49, 49, 49, 49, 48, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 350) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/350 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/350' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578148010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148010 none COc1cncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 49, 49, 29, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 49, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578148010 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 Building ZINC001578148010 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578148010 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 349) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148010.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578148010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148010 none COc1cncc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 48, 48, 48, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 49, 49, 49, 49, 49, 49, 48, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 12, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 192 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 350) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148010.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578148010.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148010 none COc1cncc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 49, 49, 49, 29, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 50, 49, 29, 29, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578148010 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148010 Building ZINC001578148011 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578148011 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 351) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/351 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/351' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578148011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148011 none COc1cncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 46, 46, 46, 28, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 16, 16, 49, 49, 49, 49, 49, 49, 46, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 352) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/352 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/352' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578148011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148011 none COc1cncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 47, 27, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 49, 49, 49, 49, 49, 49, 47, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578148011 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 Building ZINC001578148011 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578148011 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 351) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148011.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578148011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148011 none COc1cncc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 46, 46, 46, 28, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 16, 16, 49, 49, 49, 49, 49, 49, 46, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 16, 16, 16] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 196 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 352) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1) `ZINC001578148011.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578148011.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001578148011 none COc1cncc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 49, 49, 49, 49, 47, 47, 47, 27, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 49, 49, 49, 49, 49, 49, 47, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48]) total number of confs: 195 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578148011 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578148011 Building ZINC001578157489 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578157489 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 353) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/353 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/353' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578157489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157489 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 21, 21, 21, 42, 48, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 42, 42, 48, 48, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 354) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/354 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/354' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578157489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157489 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 19, 19, 19, 47, 47, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 47, 47, 47, 47, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578157489 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 Building ZINC001578157489 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578157489 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 353) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157489.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578157489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157489 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 10, 21, 21, 21, 42, 48, 50, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 42, 42, 48, 48, 50, 50, 5, 5, 5, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 354) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157489.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578157489.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157489 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 19, 19, 19, 47, 47, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 19, 47, 47, 47, 47, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578157489 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157489 Building ZINC001578157494 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578157494 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 355) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/355 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/355' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578157494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157494 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 46, 46, 48, 48, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 356) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/356 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/356' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578157494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157494 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 12, 18, 18, 18, 42, 48, 50, 50, 50, 50, 50, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 42, 42, 48, 48, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578157494 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 Building ZINC001578157494 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578157494 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 355) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/355: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157494.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578157494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157494 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 12, 16, 16, 16, 46, 48, 50, 50, 50, 50, 50, 7, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 16, 46, 46, 48, 48, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 356) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/356: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1) `ZINC001578157494.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578157494.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578157494 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)CCc1cnc[nH]1)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 6, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 12, 18, 18, 18, 42, 48, 50, 50, 50, 50, 50, 6, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 18, 42, 42, 48, 48, 50, 50, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578157494 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578157494 Building ZINC001578167286 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167286 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 357) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/357 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/357' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167286 none COc1cnc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 50, 50, 44, 44, 44, 28, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 50, 50, 50, 50, 50, 50, 44, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 358) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/358 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/358' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167286 none COc1cnc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 48, 48, 45, 45, 45, 25, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 48, 48, 50, 50, 50, 48, 45, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 48] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167286 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 Building ZINC001578167286 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167286 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 357) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167286.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167286 none COc1cnc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 44, 44, 50, 50, 44, 44, 44, 28, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 50, 50, 50, 50, 50, 50, 44, 28, 28, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 358) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167286.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167286.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167286 none COc1cnc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 48, 48, 45, 45, 45, 25, 11, 2, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 48, 48, 50, 50, 50, 48, 45, 25, 25, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 48] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 203 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167286 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167286 Building ZINC001578167288 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167288 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 359) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/359 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/359' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167288 none COc1cnc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 49, 49, 45, 45, 45, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 49, 49, 50, 50, 50, 49, 45, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 360) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/360 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/360' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cnc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167288 none COc1cnc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 49, 49, 45, 45, 45, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 49, 49, 50, 50, 50, 49, 45, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167288 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 Building ZINC001578167288 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167288 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 359) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167288.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167288 none COc1cnc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 49, 49, 45, 45, 45, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 49, 49, 50, 50, 50, 49, 45, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 214 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 360) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cnc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1) `ZINC001578167288.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167288.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578167288 none COc1cnc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)nc1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 8, 1, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 45, 49, 49, 45, 45, 45, 27, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 15, 15, 49, 49, 50, 50, 50, 49, 45, 27, 27, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15, 15, 15, 15, 49] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167288 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167288 Building ZINC001578167464 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167464 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 361) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/361 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/361' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167464 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 17, 30, 30, 30, 49, 49, 49, 49, 49, 49, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 362) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/362 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/362' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167464 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 20, 30, 30, 30, 48, 48, 48, 48, 48, 48, 8, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167464 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 Building ZINC001578167464 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167464 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 361) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167464.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167464 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 17, 30, 30, 30, 49, 49, 49, 49, 49, 49, 5, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 30, 49, 49, 49, 49, 49, 49, 49, 49, 49, 49, 7, 7, 7, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 362) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167464.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167464.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167464 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 20, 30, 30, 30, 48, 48, 48, 48, 48, 48, 8, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 20, 20, 30, 48, 48, 48, 48, 48, 48, 48, 48, 48, 48, 12, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167464 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167464 Building ZINC001578167465 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167465 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 363) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/363 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/363' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167465 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 17, 24, 24, 24, 44, 44, 44, 44, 44, 44, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 364) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/364 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/364' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167465 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 29, 29, 29, 50, 50, 50, 50, 50, 50, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167465 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 Building ZINC001578167465 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167465 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 363) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/363: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167465 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 8, 17, 24, 24, 24, 44, 44, 44, 44, 44, 44, 8, 14, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 24, 44, 44, 44, 44, 44, 44, 44, 44, 44, 44, 14, 14, 14, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 146 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 364) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/364: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1) `ZINC001578167465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578167465 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H](CNC(=O)C12CCN(CC1)C2)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 15, 29, 29, 29, 50, 50, 50, 50, 50, 50, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167465 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167465 Building ZINC001578167636 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167636 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 365) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/365 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/365' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167636 none COc1nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 22, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 48, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 366) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/366 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/366' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167636 none COc1nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 46, 46, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 50, 50, 50, 50, 50, 46, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167636 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 Building ZINC001578167636 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167636 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 365) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167636.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167636 none COc1nc(C(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 48, 48, 22, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 50, 50, 50, 50, 50, 48, 22, 22, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 11, 11, 11, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 366) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167636.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167636.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167636 none COc1nc(C(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 46, 46, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 10, 10, 50, 50, 50, 50, 50, 46, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 10, 10, 10, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167636 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167636 Building ZINC001578167638 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167638 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 367) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/367 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/367' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167638 none COc1nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 46, 46, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 50, 50, 50, 50, 50, 46, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 368) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/368 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/368' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167638 none COc1nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 49, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167638 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 Building ZINC001578167638 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578167638 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 367) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167638.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578167638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167638 none COc1nc(C(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 46, 46, 46, 21, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 8, 8, 50, 50, 50, 50, 50, 46, 21, 21, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 368) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1) `ZINC001578167638.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578167638.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578167638 none COc1nc(C(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2CC2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 1, 12, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 49, 49, 49, 23, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 50, 50, 50, 50, 50, 49, 23, 23, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 38, 39, 40, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578167638 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578167638 Building ZINC001578175540 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578175540 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 369) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/369 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/369' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578175540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175540 none Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 32, 17, 17, 17, 14, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 9, 9, 50, 50, 50, 50, 50, 34, 34, 32, 32, 17, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 370) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/370 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/370' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578175540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175540 none Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 30, 18, 18, 18, 14, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 34, 34, 30, 30, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578175540 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 Building ZINC001578175540 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578175540 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 369) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175540.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578175540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175540 none Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 32, 17, 17, 17, 14, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 9, 9, 50, 50, 50, 50, 50, 34, 34, 32, 32, 17, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 370) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175540.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578175540.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175540 none Cn1cncc1CCC(=O)NC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 30, 18, 18, 18, 14, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 7, 7, 50, 50, 50, 50, 50, 34, 34, 30, 30, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578175540 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175540 Building ZINC001578175541 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578175541 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 371) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/371 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/371' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578175541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175541 none Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 30, 20, 20, 20, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 34, 34, 30, 30, 20, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 372) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/372 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/372' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578175541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175541 none Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 34, 18, 18, 18, 14, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 34, 34, 34, 34, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578175541 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 Building ZINC001578175541 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578175541 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 371) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578175541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175541 none Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 30, 20, 20, 20, 15, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 50, 50, 50, 50, 50, 34, 34, 30, 30, 20, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 372) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1) `ZINC001578175541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578175541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578175541 none Cn1cncc1CCC(=O)NC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 34, 18, 18, 18, 14, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 50, 50, 50, 50, 50, 34, 34, 34, 34, 18, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 7] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51, 52]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578175541 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578175541 Building ZINC001578202541 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578202541 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 373) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/373 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/373' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578202541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202541 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 27, 27, 41, 50, 50, 50, 50, 19, 19, 19, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 374) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/374 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/374' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578202541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202541 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 12, 24, 24, 41, 50, 50, 50, 50, 12, 12, 12, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578202541 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 Building ZINC001578202541 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578202541 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 373) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202541.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578202541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202541 none CN(C[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 27, 27, 41, 50, 50, 50, 50, 19, 19, 19, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 179 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 374) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202541.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578202541.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202541 none CN(C[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 5, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 12, 24, 24, 41, 50, 50, 50, 50, 12, 12, 12, 5, 5, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578202541 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202541 Building ZINC001578202542 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578202542 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 375) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/375 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/375' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578202542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202542 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 13, 24, 24, 41, 50, 50, 50, 50, 13, 13, 13, 6, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 376) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/376 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/376' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578202542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202542 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 28, 28, 41, 50, 50, 50, 50, 19, 19, 19, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578202542 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 Building ZINC001578202542 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578202542 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 375) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202542.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578202542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202542 none CN(C[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 6, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 13, 24, 24, 41, 50, 50, 50, 50, 13, 13, 13, 6, 6, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 41, 42, 11, 12, 13, 14, 15, 16, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 376) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1) `ZINC001578202542.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578202542.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578202542 none CN(C[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)C(=O)Cn1cncn1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 5, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 8, 3, 3, 3, 3, 3, 3, 2, 1, 3, 1, 1, 1, 1, 1, 1, 3, 19, 28, 28, 41, 50, 50, 50, 50, 19, 19, 19, 8, 8, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 41, 41, 50, 50] 50 rigid atoms, others: [45, 43, 37, 38, 39, 40, 9, 42, 11, 12, 13, 14, 15, 16, 41, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578202542 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578202542 Building ZINC001578314314 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578314314 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 377) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/377 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/377' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001578314314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578314314 none COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 50, 18, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 35, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 378) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/378 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/378' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001578314314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578314314 none COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 50, 17, 6, 2, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 32, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578314314 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 Building ZINC001578314314 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578314314 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 377) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001578314314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578314314 none COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 50, 18, 7, 3, 7, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 50, 50, 50, 35, 18, 18, 3, 3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 169 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 378) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001578314314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578314314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578314314 none COC(=O)NCC(=O)N1C[C@H]2CC[C@@H](C1)N2C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', '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.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 5, 1, 11, 8, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 50, 17, 6, 2, 6, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 32, 17, 17, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 175 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578314314 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578314314 Building ZINC001578352533 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578352533 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 379) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/379 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/379' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1) `ZINC001578352533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578352533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578352533 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 19, 22, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 22, 22, 22, 22, 38, 38, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 380) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/380 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/380' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1) `ZINC001578352533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578352533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578352533 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 8, 8, 8, 24, 27, 31, 45, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 24, 24, 31, 31, 31, 31, 45, 45, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578352533 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 Building ZINC001578352533 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578352533 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 379) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1) `ZINC001578352533.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578352533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578352533 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 13, 19, 22, 38, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 13, 13, 22, 22, 22, 22, 38, 38, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 380) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1) `ZINC001578352533.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578352533.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578352533 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)CCCCNC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 5, 5, 5, 8, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 3, 3, 3, 3, 3, 3, 8, 8, 8, 24, 27, 31, 45, 50, 50, 50, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 8, 24, 24, 31, 31, 31, 31, 45, 45, 50, 50, 50, 3, 3] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 238 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578352533 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352533 Building ZINC001578352790 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578352790 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 381) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/381 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/381' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578352790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578352790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578352790 none Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 43, 12, 12, 12, 6, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 47, 47, 43, 43, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 382) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/382 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/382' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578352790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578352790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578352790 none Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 39, 12, 12, 12, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 45, 45, 39, 39, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578352790 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 Building ZINC001578352790 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578352790 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 381) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578352790.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578352790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578352790 none Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 43, 12, 12, 12, 6, 6, 6, 6, 6, 3, 1, 4, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 47, 47, 43, 43, 12, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 382) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578352790.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578352790.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578352790 none Cn1ncc(CCC(=O)N[C@H]2CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 8, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 45, 39, 12, 12, 12, 7, 7, 7, 7, 7, 3, 1, 5, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 45, 45, 39, 39, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578352790 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352790 Building ZINC001578352797 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578352797 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 383) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/383 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/383' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578352797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578352797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578352797 none CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 11, 11, 11, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 384) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/384 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/384' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578352797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578352797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578352797 none CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 7, 7, 7, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578352797 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 Building ZINC001578352797 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578352797 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 383) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578352797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578352797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578352797 none CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 11, 11, 11, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 11, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 224 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 384) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578352797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578352797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578352797 none CCCC(=O)NCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 1, 11, 8, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 7, 7, 7, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 7, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578352797 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578352797 Building ZINC001578353063 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578353063 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 385) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/385 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/385' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001578353063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578353063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 23, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 386) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/386 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/386' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001578353063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578353063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578353063 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 Building ZINC001578353063 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578353063 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 385) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001578353063.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578353063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353063 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 11, 23, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 11, 11, 36, 36, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 386) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1) `ZINC001578353063.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578353063.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353063 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 18, 36, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578353063 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353063 Building ZINC001578353064 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578353064 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 387) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/387 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/387' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001578353064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578353064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353064 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 388) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/388 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/388' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001578353064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578353064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353064 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 34, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578353064 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 Building ZINC001578353064 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578353064 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 387) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001578353064.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578353064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353064 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 9, 20, 39, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 9, 9, 34, 34, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 388) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1) `ZINC001578353064.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578353064.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578353064 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](NC(=O)COC[C@H]2CCOC2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 8, 14, 34, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 32, 32, 50, 50, 50, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 50, 51] set([14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578353064 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353064 Building ZINC001578353117 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578353117 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 389) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/389 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/389' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578353117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578353117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578353117 none CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 39, 12, 12, 12, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 39, 39, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 390) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/390 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/390' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578353117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578353117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578353117 none CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 25, 26, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 44, 44, 37, 37, 26, 26, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578353117 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 Building ZINC001578353117 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578353117 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 389) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578353117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578353117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578353117 none CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 39, 12, 12, 12, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 39, 39, 12, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 297 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 390) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578353117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578353117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578353117 none CC(=O)N(C)CCCC(=O)N[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 50, 25, 26, 5, 5, 5, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 50, 50, 50, 50, 50, 50, 44, 44, 37, 37, 26, 26, 5, 2, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 293 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578353117 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578353117 Building ZINC001578369419 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578369419 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 391) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/391 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/391' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001578369419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578369419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578369419 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 20, 20, 38, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 20, 20, 20, 20, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 392) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/392 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/392' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001578369419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578369419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578369419 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 11, 11, 21, 21, 39, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 21, 21, 21, 21, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578369419 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 Building ZINC001578369419 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578369419 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 391) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001578369419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578369419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578369419 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 10, 20, 20, 38, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 20, 20, 20, 20, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 392) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1) `ZINC001578369419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578369419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578369419 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCOCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 11, 11, 21, 21, 39, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 21, 21, 21, 21, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 32, 24, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578369419 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578369419 Building ZINC001578379500 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578379500 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 393) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/393 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/393' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1) `ZINC001578379500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578379500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578379500 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 17, 17, 17, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 394) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/394 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/394' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1) `ZINC001578379500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578379500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578379500 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 32, 32, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578379500 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 Building ZINC001578379500 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578379500 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 393) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/393: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1) `ZINC001578379500.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578379500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578379500 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 17, 17, 17, 31, 31, 50, 50, 50, 50, 50, 50, 50, 17, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 17, 17, 17, 17, 50, 50, 50, 50, 50, 50, 50, 17, 17] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 394) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/394: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1) `ZINC001578379500.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578379500.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578379500 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 8, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 32, 32, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 120 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578379500 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578379500 Building ZINC001578382389 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578382389 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 395) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/395 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/395' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1) `ZINC001578382389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578382389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578382389 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 396) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/396 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/396' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1) `ZINC001578382389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578382389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578382389 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578382389 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 Building ZINC001578382389 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578382389 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 395) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1) `ZINC001578382389.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578382389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578382389 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 50, 50, 50, 50, 50, 50, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 396) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1) `ZINC001578382389.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578382389.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578382389 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2n[nH]c3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'N.pl3', 'H', 'C.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 8, 8, 6, 1, 1, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 117 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578382389 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382389 Building ZINC001578382602 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578382602 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 397) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/397 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/397' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001578382602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578382602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578382602 none CCc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 26, 13, 26, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 40, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 398) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/398 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/398' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001578382602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578382602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578382602 none CCc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 25, 14, 25, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 35, 35, 35, 35, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 35, 35, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578382602 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 Building ZINC001578382602 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578382602 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 397) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/397: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001578382602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578382602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578382602 none CCc1c(C(=O)N2CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 26, 13, 26, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 40, 50, 50, 50, 50, 50, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40, 40] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 398) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/398: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C) `ZINC001578382602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578382602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001578382602 none CCc1c(C(=O)N2CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 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, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 25, 14, 25, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 35, 35, 35, 35, 50, 50, 50, 50, 50, 14, 14, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 35, 35, 35, 35] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578382602 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578382602 Building ZINC001578386657 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578386657 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 399) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/399 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/399' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1) `ZINC001578386657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578386657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578386657 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 8, 8, 22, 24, 29, 38, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 22, 22, 28, 28, 29, 29, 38, 38, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 400) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/400 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/400' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1) `ZINC001578386657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578386657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578386657 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 21, 23, 27, 36, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 21, 21, 27, 27, 27, 27, 36, 36, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578386657 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 Building ZINC001578386657 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578386657 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 399) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1) `ZINC001578386657.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578386657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578386657 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 8, 8, 22, 24, 29, 38, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 22, 22, 28, 28, 29, 29, 38, 38, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 400) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1) `ZINC001578386657.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578386657.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578386657 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)CCCCc2cnn[nH]2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 5, 1, 1, 8, 8, 8, 6, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 7, 7, 7, 7, 7, 7, 7, 21, 23, 27, 36, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 7, 7, 21, 21, 27, 27, 27, 27, 36, 36, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 214 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578386657 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386657 Building ZINC001578386837 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578386837 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 401) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/401 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/401' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1) `ZINC001578386837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578386837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578386837 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 18, 18, 18, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 402) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/402 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/402' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1) `ZINC001578386837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578386837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578386837 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 15, 15, 15, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578386837 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 Building ZINC001578386837 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578386837 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 401) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1) `ZINC001578386837.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578386837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578386837 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 18, 18, 18, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 18, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 18, 18, 18, 18, 50, 50, 50, 50, 50, 50, 50, 18, 18] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 120 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 402) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1) `ZINC001578386837.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578386837.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578386837 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2cnn3c2OCCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.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, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 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: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 15, 15, 15, 23, 23, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 15, 15, 50, 50, 50, 50, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 111 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578386837 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578386837 Building ZINC001578392052 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578392052 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 403) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/403 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/403' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1) `ZINC001578392052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578392052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578392052 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 404) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/404 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/404' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1) `ZINC001578392052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578392052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578392052 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 23, 23, 23, 23, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578392052 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 Building ZINC001578392052 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578392052 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 403) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1) `ZINC001578392052.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578392052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578392052 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 23, 23, 23, 23, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 109 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 404) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1) `ZINC001578392052.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578392052.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578392052 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)c2ccn3nnnc3c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 8, 8, 1, 1, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 20, 23, 23, 23, 23, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 23, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 23, 23, 23, 23, 50, 50, 50, 23, 23] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 112 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578392052 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392052 Building ZINC001578392159 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578392159 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 405) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/405 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/405' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1) `ZINC001578392159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578392159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578392159 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 10, 20, 20, 20, 20, 20, 37, 37, 50, 50, 50, 50, 50, 50, 50, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 406) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/406 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/406' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1) `ZINC001578392159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578392159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578392159 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 8, 19, 19, 19, 19, 19, 37, 37, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 136 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578392159 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 Building ZINC001578392159 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578392159 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 405) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/405: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1) `ZINC001578392159.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578392159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578392159 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 10, 20, 20, 20, 20, 20, 37, 37, 50, 50, 50, 50, 50, 50, 50, 20, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 20, 20, 20, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 132 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 406) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/406: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1) `ZINC001578392159.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578392159.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578392159 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CCN(C(=O)[C@@]23CCN(C2)CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 5, 5, 10, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 1, 1, 1, 5, 5, 8, 19, 19, 19, 19, 19, 37, 37, 50, 50, 50, 50, 50, 50, 50, 19, 2, 2, 2, 2, 2, 2, 2, 2, 2, 5, 19, 19, 19, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 19] 50 rigid atoms, others: [1, 4, 5, 6] set([0, 2, 3, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 136 number of broken/clashed sets: 30 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578392159 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578392159 Building ZINC001578393757 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578393757 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 407) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/407 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/407' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578393757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578393757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578393757 none Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 40, 16, 12, 16, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 40, 40, 40, 40, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 408) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/408 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/408' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578393757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578393757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578393757 none Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 35, 16, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 35, 35, 35, 35, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578393757 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 Building ZINC001578393757 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578393757 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 407) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578393757.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578393757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578393757 none Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 40, 40, 16, 12, 16, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 40, 40, 40, 40, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 408) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578393757.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578393757.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578393757 none Cn1cncc1CCC(=O)N1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 8, 1, 1, 5, 5, 1, 11, 8, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 35, 35, 16, 13, 16, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 35, 35, 35, 35, 13, 13, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578393757 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578393757 Building ZINC001578472363 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472363 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 409) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/409 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/409' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578472363 none Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 410) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/410 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/410' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578472363 none Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472363 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 Building ZINC001578472363 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472363 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 409) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472363.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578472363 none Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 410) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472363.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472363.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578472363 none Cn1c(=O)cccc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 1, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 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/167320/xcr-8058097.70/working/building/ZINC001578472363 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472363 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472363 Building ZINC001578472419 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472419 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 411) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/411 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/411' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1) `ZINC001578472419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578472419 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 38, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 412) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/412 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/412' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1) `ZINC001578472419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578472419 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472419 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 Building ZINC001578472419 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472419 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 411) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/411: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1) `ZINC001578472419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578472419 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 38, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 412) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/412: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1) `ZINC001578472419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578472419 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnn3c2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', '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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472419 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472419 Building ZINC001578472511 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472511 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 413) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/413 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/413' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472511 none CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 18, 18, 18, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 18, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 414) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/414 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/414' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472511 none CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 19, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472511 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 Building ZINC001578472511 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472511 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 413) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472511.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472511 none CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 18, 18, 18, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 18, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 414) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472511.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472511.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472511 none CN1C(=O)CC[C@@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 19, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472511 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472511 Building ZINC001578472512 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472512 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 415) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/415 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/415' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472512 none CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 19, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 416) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/416 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/416' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472512 none CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472512 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 Building ZINC001578472512 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472512 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 415) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472512.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472512 none CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 19, 19, 19, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 50, 50, 43, 43, 19, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 416) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472512.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472512.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472512 none CN1C(=O)CC[C@H]1CC(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 20, 20, 20, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 43, 43, 20, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472512 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472512 Building ZINC001578472697 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472697 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 417) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/417 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/417' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578472697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578472697 none CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 35, 50, 35, 35, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 418) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/418 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/418' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578472697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578472697 none CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 33, 50, 33, 33, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472697 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 Building ZINC001578472697 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472697 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 417) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/417: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578472697.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578472697 none CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 35, 50, 35, 35, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 418) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/418: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578472697.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472697.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578472697 none CC(C)[C@@H](C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 33, 50, 33, 33, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 223 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472697 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472697 Building ZINC001578472704 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472704 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 419) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/419 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/419' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578472704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578472704 none Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 47, 25, 25, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 48, 48, 47, 47, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 420) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/420 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/420' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578472704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578472704 none Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 47, 25, 25, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472704 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 Building ZINC001578472704 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472704 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 419) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578472704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578472704 none Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 47, 25, 25, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 48, 48, 47, 47, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 420) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578472704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578472704 none Cn1ccc(CCC(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 5, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 47, 25, 25, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 47, 47, 47, 47, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472704 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472704 Building ZINC001578472982 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472982 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 421) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/421 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/421' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472982 none CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 38, 49, 37, 37, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 49, 49, 49, 49, 49, 49, 37, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 422) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/422 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/422' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472982 none CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 33, 49, 32, 32, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 49, 49, 49, 49, 49, 49, 32, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472982 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 Building ZINC001578472982 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578472982 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 421) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/421: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472982.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578472982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472982 none CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 38, 49, 37, 37, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 49, 49, 49, 49, 49, 49, 37, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 151 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 422) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/422: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578472982.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578472982.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578472982 none CC(=O)N1CCC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 33, 49, 32, 32, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 49, 49, 49, 49, 49, 49, 32, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 149 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578472982 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578472982 Building ZINC001578473012 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473012 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 423) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/423 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/423' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578473012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001578473012 none COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', '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, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 44, 44, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 44, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 424) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/424 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/424' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578473012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001578473012 none COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', '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, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 45, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473012 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 Building ZINC001578473012 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473012 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 423) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578473012.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001578473012 none COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', '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, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 44, 44, 44, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 44, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 424) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578473012.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473012.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001578473012 none COc1nccc(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', '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, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 3, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 45, 45, 45, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 45, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45]) total number of confs: 131 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473012 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473012 Building ZINC001578473308 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473308 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 425) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/425 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/425' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1) `ZINC001578473308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578473308 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 426) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/426 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/426' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1) `ZINC001578473308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578473308 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473308 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 Building ZINC001578473308 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473308 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 425) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1) `ZINC001578473308.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578473308 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 426) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1) `ZINC001578473308.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473308.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578473308 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2nc3ncccn3n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 8, 1, 8, 1, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 30, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 30, 50, 50, 50, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 127 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473308 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473308 Building ZINC001578473652 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473652 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 427) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/427 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/427' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001578473652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578473652 none Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 42, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 428) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/428 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/428' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001578473652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578473652 none Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 42, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473652 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 Building ZINC001578473652 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473652 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 427) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001578473652.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578473652 none Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 42, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 428) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1) `ZINC001578473652.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473652.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578473652 none Cn1ccc(=O)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 42, 42, 42, 17, 17, 17, 17, 4, 17, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 50, 50, 50, 50, 50, 50, 42, 17, 17, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001578473652 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473652 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473652 Building ZINC001578473660 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473660 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 429) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/429 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/429' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1) `ZINC001578473660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578473660 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 48, 48, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 430) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/430 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/430' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1) `ZINC001578473660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578473660 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 48, 48, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473660 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 Building ZINC001578473660 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473660 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 429) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/429: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1) `ZINC001578473660.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578473660 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 48, 48, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 430) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/430: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1) `ZINC001578473660.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473660.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578473660 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CCn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 27, 48, 48, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473660 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473660 Building ZINC001578473734 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473734 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 431) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/431 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/431' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 432) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/432 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/432' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 433) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/433 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/433' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 434) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/434 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/434' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473734 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 Building ZINC001578473734 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473734 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 431) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 432) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 433) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 434) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473734 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 Building ZINC001578473734 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473734 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 431) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 432) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 433) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 434) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473734 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 Building ZINC001578473734 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473734 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 431) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 432) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 44, 50, 32, 32, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 32, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 137 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 433) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/433: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 434) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/434: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473734.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473734.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473734 none CCN1CCOC[C@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 42, 50, 33, 33, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 135 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473734 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473734 Building ZINC001578473736 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473736 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 435) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/435 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/435' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 436) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/436 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/436' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 437) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/437 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/437' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 438) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/438 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/438' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473736 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 Building ZINC001578473736 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473736 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 435) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 436) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 437) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 438) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473736 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 Building ZINC001578473736 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473736 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 435) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 436) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 437) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 438) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473736 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 Building ZINC001578473736 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578473736 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 435) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 436) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 35, 50, 35, 35, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 437) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/437: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 438) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/438: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578473736.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578473736.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578473736 none CCN1CCOC[C@@H]1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 10, 5, 5, 12, 5, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 41, 50, 41, 41, 15, 15, 15, 15, 4, 15, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 15, 15, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 15] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 151 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473736 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473736 Building ZINC001578473751 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473751 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 439) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/439 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/439' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1) `ZINC001578473751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473751 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 440) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/440 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/440' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1) `ZINC001578473751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473751 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473751 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 Building ZINC001578473751 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473751 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 439) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1) `ZINC001578473751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473751 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 440) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1) `ZINC001578473751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473751 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473751 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473751 Building ZINC001578473753 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473753 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 441) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/441 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/441' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1) `ZINC001578473753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473753 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 442) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/442 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/442' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1) `ZINC001578473753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473753 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473753 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 Building ZINC001578473753 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578473753 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 441) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1) `ZINC001578473753.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578473753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473753 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 22, 50, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 442) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1) `ZINC001578473753.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578473753.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578473753 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)[C@@H]2CCc3nccn3C2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 8, 1, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 21, 21, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 21, 50, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001578473753 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578473753 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578473753 Building ZINC001578474165 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474165 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 443) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/443 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/443' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578474165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474165 none Cn1cc(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 36, 36, 36, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 46, 46, 46, 46, 50, 50, 46, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 444) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/444 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/444' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578474165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474165 none Cn1cc(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 36, 36, 36, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 46, 46, 46, 46, 50, 50, 46, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474165 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 Building ZINC001578474165 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474165 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 443) grep: /scratch/xiaobo/167320/xcr-8058097.70/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(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578474165.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474165 none Cn1cc(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 36, 36, 36, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 46, 46, 46, 46, 50, 50, 46, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 444) grep: /scratch/xiaobo/167320/xcr-8058097.70/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(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578474165.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474165.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474165 none Cn1cc(C(N)=O)cc1C(=O)N[C@H]1C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 1, 8, 11, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 6, 6, 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, 4, 6, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 46, 36, 36, 36, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 46, 46, 46, 46, 50, 50, 46, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 138 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474165 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474165 Building ZINC001578474197 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474197 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 445) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/445 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/445' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578474197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578474197 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 446) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/446 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/446' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578474197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578474197 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474197 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 Building ZINC001578474197 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474197 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 445) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578474197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578474197 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 446) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578474197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578474197 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474197 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474197 Building ZINC001578474217 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474217 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 447) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/447 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/447' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1) `ZINC001578474217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474217 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 448) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/448 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/448' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1) `ZINC001578474217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474217 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474217 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 Building ZINC001578474217 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474217 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 447) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1) `ZINC001578474217.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474217 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 129 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 448) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1) `ZINC001578474217.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474217.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474217 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)c2cnc3n2CCC3)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 39, 39, 39, 50, 50, 50, 50, 50, 50, 50, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 39, 50, 50, 50, 50, 50, 50, 50, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474217 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474217 Building ZINC001578474258 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474258 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 449) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/449 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/449' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578474258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474258 none CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 34, 34, 34, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 50, 50, 50, 50, 50, 39, 39, 39, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 450) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/450 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/450' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578474258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474258 none CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 34, 34, 34, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 50, 50, 50, 50, 50, 39, 39, 39, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474258 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 Building ZINC001578474258 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474258 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 449) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/449: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578474258.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474258 none CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 34, 34, 34, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 50, 50, 50, 50, 50, 39, 39, 39, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 450) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/450: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001578474258.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474258.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001578474258 none CCn1nc(C)c(C(=O)N[C@H]2C[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 34, 34, 34, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 39, 50, 50, 50, 50, 50, 39, 39, 39, 34, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474258 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474258 Building ZINC001578474342 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474342 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 451) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/451 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/451' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1) `ZINC001578474342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474342 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 17, 17, 17, 39, 40, 40, 40, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 39, 39, 40, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 452) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/452 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/452' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1) `ZINC001578474342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474342 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 19, 19, 19, 41, 41, 41, 41, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 41, 41, 41, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474342 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 Building ZINC001578474342 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578474342 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 451) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1) `ZINC001578474342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578474342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474342 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 17, 17, 17, 39, 40, 40, 40, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 17, 39, 39, 40, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 452) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1) `ZINC001578474342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578474342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578474342 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@H](NC(=O)CNC(=O)c2ccoc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.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'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 11, 1, 1, 1, 12, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 8, 8, 8, 8, 8, 19, 19, 19, 41, 41, 41, 41, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 19, 41, 41, 41, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578474342 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578474342 Building ZINC001578530403 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530403 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 453) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/453 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/453' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 454) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/454 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/454' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 455) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/455 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/455' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 456) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/456 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/456' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530403 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 Building ZINC001578530403 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530403 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 453) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 454) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 455) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 456) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530403 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 Building ZINC001578530403 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530403 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 453) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 454) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 455) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 456) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530403 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 Building ZINC001578530403 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530403 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 453) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 454) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [16, 16, 16, 16, 14, 3, 14, 1, 1, 1, 8, 8, 8, 8, 8, 16, 16, 16, 31, 16, 16, 16, 16, 16, 16, 16, 16, 8, 8, 31, 31, 31, 31, 16, 16] 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]) total number of confs: 114 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 455) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/455: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 456) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/456: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1) `ZINC001578530403.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530403.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530403 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 17, 2, 18, 1, 1, 1, 8, 8, 8, 8, 8, 21, 21, 21, 31, 21, 21, 21, 21, 21, 21, 21, 21, 8, 8, 31, 31, 31, 31, 21, 21] 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530403 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530403 Building ZINC001578530405 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530405 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 457) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/457 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/457' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 458) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/458 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/458' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 459) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/459 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/459' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 460) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/460 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/460' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530405 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 Building ZINC001578530405 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530405 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 457) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 458) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 459) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 460) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530405 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 Building ZINC001578530405 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530405 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 457) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 458) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 459) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 460) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530405 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 Building ZINC001578530405 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001578530405 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 457) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 458) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 10, 10, 10, 10, 10, 11, 11, 11, 27, 11, 11, 11, 11, 11, 11, 11, 11, 10, 10, 27, 27, 27, 27, 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]) total number of confs: 103 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 459) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/459: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 460) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/460: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1) `ZINC001578530405.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001578530405.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 38 natoms 37 natoms 36 natoms 35 names: ZINC001578530405 none CN1CCN(C(=O)[C@]([O-])([SiH3])c2ccc(Br)s2)[C@@H](CN)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', '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, 17, 14, 5, 7, 5, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 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] 0 hydrogens 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, 6, 1, 6, 1, 1, 1, 11, 11, 11, 11, 11, 13, 13, 13, 33, 13, 13, 13, 13, 13, 13, 13, 13, 11, 11, 33, 33, 33, 33, 13, 13] 50 rigid atoms, others: [8, 9, 5, 7] set([0, 1, 2, 3, 4, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578530405 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578530405 Building ZINC001578649559 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578649559 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 461) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/461 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/461' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578649559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649559 none CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 29, 19, 13, 19, 19, 5, 4, 5, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 29, 29, 57, 13, 13, 5, 5, 5, 8, 8] 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]) total number of confs: 205 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 462) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/462 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/462' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578649559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649559 none CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 13, 18, 18, 5, 4, 5, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 54, 13, 13, 5, 5, 5, 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]) total number of confs: 197 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578649559 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 Building ZINC001578649559 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578649559 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 461) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/461: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578649559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649559 none CNC[C@@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [30, 29, 19, 13, 19, 19, 5, 4, 5, 1, 4, 1, 1, 1, 8, 8, 8, 8, 8, 30, 30, 30, 30, 29, 29, 57, 13, 13, 5, 5, 5, 8, 8] 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]) total number of confs: 205 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 462) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/462: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578649559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649559 none CNC[C@@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [29, 29, 18, 13, 18, 18, 5, 4, 5, 1, 4, 1, 1, 1, 4, 4, 4, 4, 4, 29, 29, 29, 29, 29, 29, 54, 13, 13, 5, 5, 5, 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]) total number of confs: 197 number of broken/clashed sets: 32 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578649559 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649559 Building ZINC001578649560 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578649560 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 463) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/463 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/463' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578649560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649560 none CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 30, 22, 16, 22, 22, 8, 5, 8, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 30, 30, 66, 16, 16, 8, 8, 8, 5, 5] 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]) total number of confs: 212 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 464) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/464 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/464' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578649560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649560 none CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 30, 21, 15, 21, 21, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 32, 32, 30, 30, 63, 15, 15, 7, 7, 7, 6, 6] 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]) total number of confs: 210 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578649560 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 Building ZINC001578649560 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578649560 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 463) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578649560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649560 none CNC[C@H](O)CN(C)C(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 30, 22, 16, 22, 22, 8, 5, 8, 1, 5, 1, 1, 1, 5, 5, 5, 5, 5, 31, 31, 31, 31, 30, 30, 66, 16, 16, 8, 8, 8, 5, 5] 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]) total number of confs: 212 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 464) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001578649560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578649560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 36 natoms 35 natoms 34 natoms 33 names: ZINC001578649560 none CNC[C@H](O)CN(C)C(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 10, 5, 5, 7, 12, 5, 8, 5, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [32, 30, 21, 15, 21, 21, 7, 4, 7, 1, 4, 1, 1, 1, 6, 6, 6, 6, 6, 32, 32, 32, 32, 30, 30, 63, 15, 15, 7, 7, 7, 6, 6] 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]) total number of confs: 210 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578649560 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578649560 Building ZINC001578712198 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578712198 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 465) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/465 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/465' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1) `ZINC001578712198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578712198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578712198 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 466) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/466 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/466' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1) `ZINC001578712198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578712198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578712198 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578712198 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 Building ZINC001578712198 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578712198 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 465) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/465: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1) `ZINC001578712198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578712198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578712198 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 466) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/466: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1) `ZINC001578712198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578712198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578712198 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC1C[C@H]2CC[C@@H](C1)N2C(=O)Cn1nccn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 9, 22, 22, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 9, 9, 9, 50, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578712198 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578712198 Building ZINC001578736501 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578736501 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 467) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/467 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/467' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1) `ZINC001578736501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578736501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001578736501 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 8, 6, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 18, 8, 8, 22, 22, 22, 22, 22, 8, 5, 5, 11, 11, 11, 11, 11, 5, 2, 8, 8, 18, 18, 18, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 468) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/468 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/468' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1) `ZINC001578736501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578736501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001578736501 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 8, 6, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 18, 8, 8, 20, 20, 20, 20, 20, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 18, 18, 18, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578736501 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 Building ZINC001578736501 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578736501 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 467) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1) `ZINC001578736501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578736501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001578736501 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 8, 6, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 8, 18, 8, 8, 22, 22, 22, 22, 22, 8, 5, 5, 11, 11, 11, 11, 11, 5, 2, 8, 8, 18, 18, 18, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 91 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 468) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1) `ZINC001578736501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578736501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 43 natoms 42 natoms 41 natoms 40 names: ZINC001578736501 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(OC)c(c3nn[nH]n3)c2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.3', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 12, 5, 1, 1, 8, 8, 8, 6, 8, 1, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 5, 5, 5, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 18, 8, 8, 20, 20, 20, 20, 20, 8, 5, 5, 10, 10, 10, 10, 10, 5, 2, 8, 8, 18, 18, 18, 8, 5] 50 rigid atoms, others: [4, 5, 6, 7] set([0, 1, 2, 3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 83 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578736501 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578736501 Building ZINC001578737266 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578737266 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 469) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/469 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/469' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)cn1) `ZINC001578737266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578737266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001578737266 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)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', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 6, 6, 22, 22, 22, 22, 22, 6, 2, 8, 8, 8, 8, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 470) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/470 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/470' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)cn1) `ZINC001578737266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578737266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001578737266 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)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', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 8, 8, 6, 6, 23, 23, 23, 23, 23, 6, 2, 8, 8, 8, 8, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578737266 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 Building ZINC001578737266 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578737266 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 469) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/469: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)cn1) `ZINC001578737266.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578737266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001578737266 none CCn1cc([C@@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)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', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 22, 22, 22, 22, 22, 8, 8, 6, 6, 22, 22, 22, 22, 22, 6, 2, 8, 8, 8, 8, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 470) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/470: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)cn1) `ZINC001578737266.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578737266.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 41 natoms 40 natoms 39 natoms 38 names: ZINC001578737266 none CCn1cc([C@]([O-])([SiH3])C(=O)Nc2ccc(F)c(c3nn[nH]n3)c2N)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', 'F', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.pl3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 5, 12, 1, 11, 8, 1, 1, 1, 1, 15, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 6, 7] dock color type numbers: [7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 6, 6, 6, 1, 1, 1, 1, 2, 2, 2, 8, 8, 8, 8, 8, 8, 19, 19, 19, 19, 19, 8, 8, 6, 6, 23, 23, 23, 23, 23, 6, 2, 8, 8, 8, 8, 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]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578737266 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737266 Building ZINC001578737880 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578737880 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 471) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/471 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/471' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)c2)cn1) `ZINC001578737880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578737880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001578737880 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'F', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 15, 1, 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, 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: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 7, 7, 7, 7, 7, 4, 2, 11, 11, 22, 22, 22, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 472) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/472 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/472' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)c2)cn1) `ZINC001578737880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578737880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001578737880 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'F', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 15, 1, 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, 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: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 7, 7, 7, 7, 7, 4, 2, 11, 11, 23, 23, 23, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578737880 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 Building ZINC001578737880 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578737880 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 471) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)c2)cn1) `ZINC001578737880.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578737880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001578737880 none CCn1cc([C@@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'F', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 15, 1, 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, 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: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 4, 4, 7, 7, 7, 7, 7, 4, 2, 11, 11, 22, 22, 22, 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]) total number of confs: 77 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 472) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)c2)cn1) `ZINC001578737880.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578737880.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 5 is the cov attach 4 5 0 4 5 1 4 5 2 3 5 2 8 to be deleted 9 to be deleted 10 to be deleted natoms 42 natoms 41 natoms 40 natoms 39 names: ZINC001578737880 none CCn1cc([C@]([O-])([SiH3])C(=O)NCc2ccc(c3nn[nH]n3)c(F)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.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'F', 'C.ar', '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, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 15, 1, 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, 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: [7, 4, 4, 4, 1, 1, 1, 1, 2, 2, 2, 11, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 4, 4, 7, 7, 7, 7, 7, 4, 2, 11, 11, 23, 23, 23, 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]) total number of confs: 79 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578737880 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578737880 Building ZINC001578791834 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578791834 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 473) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/473 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/473' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578791834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791834 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 18, 18, 17, 4, 1, 5, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 18, 18, 18, 18, 18, 27, 27, 27, 18, 18, 4, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 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, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 474) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/474 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/474' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578791834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791834 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 26, 14, 14, 14, 4, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 26, 26, 26, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578791834 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 Building ZINC001578791834 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578791834 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 473) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578791834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791834 none COC(=O)[C@@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 27, 18, 18, 17, 4, 1, 5, 1, 1, 1, 4, 4, 8, 8, 4, 8, 8, 8, 18, 18, 18, 18, 18, 27, 27, 27, 18, 18, 4, 8, 8, 8, 8, 8, 8, 8, 8, 18, 18, 18, 18, 18, 18, 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, 44, 45, 46]) total number of confs: 97 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 474) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578791834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791834 none COC(=O)[C@@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 26, 14, 14, 14, 4, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 26, 26, 26, 14, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 14] 50 rigid atoms, others: [8, 10, 11, 12] set([0, 1, 2, 3, 4, 5, 6, 7, 9, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 68 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578791834 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791834 Building ZINC001578791835 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578791835 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 475) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/475 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/475' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578791835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791835 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 25, 18, 18, 16, 2, 1, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 15, 18, 18, 18, 18, 25, 25, 25, 18, 18, 3, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 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, 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/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 476) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/476 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/476' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578791835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791835 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 26, 20, 20, 18, 2, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 20, 20, 20, 20, 26, 26, 26, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20] 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578791835 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 Building ZINC001578791835 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578791835 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 475) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578791835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791835 none COC(=O)[C@H]1CN(C(=O)[C@@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 25, 18, 18, 16, 2, 1, 8, 1, 1, 1, 3, 3, 5, 5, 3, 5, 5, 5, 15, 18, 18, 18, 18, 25, 25, 25, 18, 18, 3, 5, 5, 5, 5, 5, 5, 5, 5, 18, 18, 18, 18, 18, 18, 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, 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/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 476) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2) `ZINC001578791835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578791835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 10 is the cov attach 4 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: ZINC001578791835 none COC(=O)[C@H]1CN(C(=O)[C@]([O-])([SiH3])c2ccc3c(c2)CCC3)CC12CNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 11, 5, 7, 5, 8, 1, 11, 5, 12, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 10, 5, 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, 5, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 20, 26, 20, 20, 18, 2, 1, 6, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 14, 20, 20, 20, 20, 26, 26, 26, 20, 20, 4, 4, 4, 4, 4, 4, 4, 4, 4, 20, 20, 20, 20, 20, 20, 20] 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: 97 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578791835 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578791835 Building ZINC001578792847 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578792847 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 477) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/477 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/477' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578792847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578792847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578792847 none CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 33, 50, 33, 33, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 478) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/478 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/478' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578792847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578792847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578792847 none CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 35, 50, 35, 35, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578792847 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 Building ZINC001578792847 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578792847 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 477) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/477: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578792847.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578792847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578792847 none CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 33, 50, 33, 33, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 478) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/478: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001578792847.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578792847.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001578792847 none CC(C)[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 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, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 50, 50, 35, 50, 35, 35, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578792847 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792847 Building ZINC001578792892 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578792892 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 479) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/479 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/479' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1) `ZINC001578792892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578792892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578792892 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 12, 12, 12, 45, 29, 48, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 12, 45, 45, 46, 46, 46, 44, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 480) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/480 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/480' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1) `ZINC001578792892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578792892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578792892 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 12, 12, 12, 45, 29, 48, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 12, 45, 45, 46, 46, 44, 46, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578792892 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 Building ZINC001578792892 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578792892 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 479) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/479: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1) `ZINC001578792892.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578792892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578792892 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 12, 12, 12, 45, 29, 48, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 12, 45, 45, 46, 46, 46, 44, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 480) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/480: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1) `ZINC001578792892.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578792892.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578792892 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCCn2ccnn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 6, 6, 6, 6, 6, 12, 12, 12, 45, 29, 48, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 12, 45, 45, 46, 46, 44, 46, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 282 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578792892 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578792892 Building ZINC001578793032 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793032 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 481) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/481 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/481' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578793032 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 48, 50, 40, 40, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 40, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 482) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/482 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/482' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578793032 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 50, 36, 36, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793032 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 Building ZINC001578793032 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793032 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 481) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793032.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578793032 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 48, 50, 40, 40, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 40, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 482) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793032.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793032.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578793032 none C[C@@H]1OCCO[C@@H]1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 12, 5, 5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 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] dock color type numbers: [7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 50, 36, 36, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 50, 36, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793032 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793032 Building ZINC001578793440 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793440 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 483) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/483 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/483' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1) `ZINC001578793440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578793440 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 34, 34, 34, 40, 40, 40, 50, 50, 40, 40, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 34, 40, 50, 50, 40, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 484) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/484 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/484' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1) `ZINC001578793440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578793440 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 34, 34, 34, 40, 40, 40, 50, 50, 40, 40, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 34, 40, 50, 50, 40, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793440 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 Building ZINC001578793440 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793440 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 483) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1) `ZINC001578793440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578793440 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 34, 34, 34, 40, 40, 40, 50, 50, 40, 40, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 34, 40, 50, 50, 40, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 484) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1) `ZINC001578793440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578793440 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cc(C(N)=O)co2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 11, 1, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 14, 14, 14, 14, 14, 34, 34, 34, 40, 40, 40, 50, 50, 40, 40, 14, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 34, 40, 50, 50, 40, 14, 14] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793440 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793440 Building ZINC001578793775 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793775 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 485) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/485 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/485' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793775 none CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 47, 50, 50, 28, 28, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 486) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/486 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/486' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793775 none CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 46, 46, 50, 50, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793775 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 Building ZINC001578793775 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793775 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 485) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793775.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793775 none CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 28, 47, 47, 50, 50, 28, 28, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 47, 47, 47, 47, 47, 47, 47, 47, 47, 50, 50, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 486) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793775.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793775.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793775 none CC(C)C[C@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 46, 46, 50, 50, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 46, 46, 46, 46, 46, 46, 46, 46, 46, 50, 50, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793775 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793775 Building ZINC001578793776 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793776 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 487) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/487 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/487' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793776 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 50, 50, 50, 50, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 488) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/488 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/488' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793776 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 48, 48, 50, 50, 31, 31, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 48, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793776 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 Building ZINC001578793776 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578793776 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 487) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793776.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578793776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793776 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 50, 50, 50, 50, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 180 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 488) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578793776.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578793776.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578793776 none CC(C)C[C@@H](C(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 7, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 31, 48, 48, 50, 50, 31, 31, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 48, 48, 48, 48, 48, 48, 48, 48, 48, 50, 50, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [50, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578793776 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578793776 Building ZINC001578798961 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578798961 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 489) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/489 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/489' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001578798961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578798961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001578798961 none COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 27, 27, 50, 50, 50, 50, 50, 27, 27, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 490) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/490 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/490' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001578798961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578798961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001578798961 none COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 27, 27, 50, 50, 50, 50, 50, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578798961 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 Building ZINC001578798961 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578798961 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 489) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001578798961.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578798961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001578798961 none COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 27, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 27, 27, 50, 50, 50, 50, 50, 27, 27, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 490) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1) `ZINC001578798961.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578798961.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001578798961 none COCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)no1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 12, 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, 3, 7, 7, 7, 7, 7, 6, 4, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 27, 27, 27, 27, 27, 27, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 27, 27, 50, 50, 50, 50, 50, 27, 27, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578798961 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798961 Building ZINC001578798974 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578798974 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 491) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/491 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/491' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578798974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798974 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 32, 32, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 492) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/492 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/492' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578798974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798974 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 31, 31, 31, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578798974 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 Building ZINC001578798974 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578798974 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 491) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798974.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578798974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798974 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 32, 32, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 32, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 492) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798974.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578798974.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798974 none CN1CC[C@@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 50, 31, 31, 31, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 48, 48, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578798974 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798974 Building ZINC001578798975 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578798975 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 493) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/493 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/493' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578798975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798975 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 30, 30, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 494) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/494 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/494' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578798975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798975 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 31, 31, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578798975 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 Building ZINC001578798975 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578798975 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 493) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798975.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578798975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798975 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 30, 30, 30, 12, 12, 12, 12, 3, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 494) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O) `ZINC001578798975.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578798975.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001578798975 none CN1CC[C@H](CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)C1=O NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 5, 7, 5, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 11, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 31, 31, 31, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 49, 49, 31, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578798975 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578798975 Building ZINC001578799092 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799092 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 495) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/495 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/495' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799092 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 25, 39, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 39, 50, 50, 50, 50, 50, 39, 39, 39, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 496) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/496 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/496' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799092 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 40, 27, 27, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 50, 50, 50, 50, 50, 40, 40, 40, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799092 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 Building ZINC001578799092 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799092 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 495) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799092.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799092 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 25, 39, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 39, 50, 50, 50, 50, 50, 39, 39, 39, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 496) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799092.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799092.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799092 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 40, 27, 27, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 50, 50, 50, 50, 50, 40, 40, 40, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799092 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799092 Building ZINC001578799093 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799093 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 497) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/497 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/497' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799093 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 29, 39, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 39, 50, 50, 50, 50, 50, 39, 39, 39, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 498) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/498 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/498' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799093 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 40, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 50, 50, 50, 50, 50, 40, 40, 40, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799093 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 Building ZINC001578799093 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799093 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 497) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799093.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799093 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 29, 39, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 39, 50, 50, 50, 50, 50, 39, 39, 39, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 498) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1) `ZINC001578799093.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799093.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799093 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 40, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 50, 50, 50, 50, 50, 40, 40, 40, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799093 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799093 Building ZINC001578799094 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799094 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 499) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/499 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/499' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799094 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 40, 27, 27, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 50, 50, 50, 50, 50, 40, 40, 40, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 500) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/500 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/500' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799094 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 25, 39, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 39, 50, 50, 50, 50, 50, 39, 39, 39, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799094 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 Building ZINC001578799094 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799094 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 499) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799094.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799094 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 27, 40, 27, 27, 13, 13, 13, 13, 3, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 50, 50, 50, 50, 50, 40, 40, 40, 27, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 500) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799094.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799094.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799094 none CO[C@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 25, 39, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 39, 50, 50, 50, 50, 50, 39, 39, 39, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799094 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799094 Building ZINC001578799095 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799095 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 501) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/501 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/501' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799095 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 40, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 50, 50, 50, 50, 50, 40, 40, 40, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 502) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/502 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/502' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799095 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 29, 39, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 39, 50, 50, 50, 50, 50, 39, 39, 39, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799095 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 Building ZINC001578799095 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799095 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 501) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799095.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799095 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 40, 25, 25, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 40, 50, 50, 50, 50, 50, 40, 40, 40, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 502) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1) `ZINC001578799095.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799095.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578799095 none CO[C@@H](C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [39, 39, 29, 39, 29, 29, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 39, 50, 50, 50, 50, 50, 39, 39, 39, 29, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799095 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799095 Building ZINC001578799109 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799109 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 503) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/503 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/503' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001578799109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799109 none CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 50, 40, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 504) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/504 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/504' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001578799109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799109 none CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 50, 40, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799109 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 Building ZINC001578799109 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799109 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 503) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001578799109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799109 none CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 50, 40, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 504) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1) `ZINC001578799109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799109 none CCc1cc(C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n(C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 5, 8, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 40, 40, 40, 38, 38, 38, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 40, 40, 40, 50, 50, 50, 50, 50, 40, 38, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13, 40, 40, 40] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799109 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799109 Building ZINC001578799171 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799171 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 505) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/505 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/505' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1) `ZINC001578799171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799171 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 27, 47, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 47, 47, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 506) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/506 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/506' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1) `ZINC001578799171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799171 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 26, 26, 26, 47, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 47, 47, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799171 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 Building ZINC001578799171 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799171 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 505) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1) `ZINC001578799171.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799171 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 27, 47, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 47, 47, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 506) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1) `ZINC001578799171.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799171.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799171 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)Cn2cc(Cl)cn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'Cl', 'C.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 8, 1, 1, 16, 1, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 26, 26, 26, 47, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 26, 47, 47, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799171 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799171 Building ZINC001578799247 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799247 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 507) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/507 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/507' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799247 none C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 32, 38, 38, 39, 50, 50, 50, 32, 32, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 38, 38, 38, 39, 39, 50, 50, 50, 32, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 508) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/508 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/508' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799247 none C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 35, 35, 36, 50, 50, 50, 30, 30, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 36, 36, 50, 50, 50, 30, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799247 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 Building ZINC001578799247 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799247 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 507) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799247.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799247 none C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [38, 32, 38, 38, 39, 50, 50, 50, 32, 32, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 38, 38, 38, 39, 39, 50, 50, 50, 32, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 508) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799247.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799247.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799247 none C[C@@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 30, 35, 35, 36, 50, 50, 50, 30, 30, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 35, 35, 35, 36, 36, 50, 50, 50, 30, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799247 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799247 Building ZINC001578799248 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799248 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 509) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/509 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/509' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799248 none C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 34, 34, 35, 50, 50, 50, 29, 29, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 34, 34, 34, 35, 35, 50, 50, 50, 29, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 510) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/510 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/510' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799248 none C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 37, 37, 38, 50, 50, 50, 31, 31, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 38, 38, 50, 50, 50, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799248 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 Building ZINC001578799248 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799248 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 509) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799248.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799248 none C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [34, 29, 34, 34, 35, 50, 50, 50, 29, 29, 13, 13, 13, 13, 4, 13, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 34, 34, 34, 35, 35, 50, 50, 50, 29, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 13] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 208 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 510) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799248.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799248.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799248 none C[C@H](CS(C)(=O)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 14, 5, 11, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 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, 3, 3, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 31, 37, 37, 38, 50, 50, 50, 31, 31, 12, 12, 12, 12, 4, 12, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 37, 37, 37, 38, 38, 50, 50, 50, 31, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799248 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799248 Building ZINC001578799274 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799274 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 511) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/511 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/511' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1) `ZINC001578799274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799274 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 28, 28, 28, 30, 30, 31, 50, 50, 50, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 30, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 512) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/512 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/512' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1) `ZINC001578799274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799274 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 28, 28, 28, 32, 32, 32, 50, 50, 50, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 32, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799274 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 Building ZINC001578799274 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799274 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 511) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/511: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1) `ZINC001578799274.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799274 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 28, 28, 28, 30, 30, 31, 50, 50, 50, 30, 30, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 28, 30, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 145 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 512) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/512: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1) `ZINC001578799274.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799274.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578799274 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cn(C3CCC3)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 9, 9, 9, 9, 9, 28, 28, 28, 32, 32, 32, 50, 50, 50, 32, 32, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 28, 32, 50, 50, 50, 50, 50, 50, 50, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799274 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799274 Building ZINC001578799293 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799293 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 513) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/513 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/513' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578799293 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 20, 32, 32, 40, 40, 40, 20, 20, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 260 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 514) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/514 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/514' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578799293 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 19, 38, 38, 42, 42, 42, 19, 19, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799293 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 Building ZINC001578799293 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799293 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 513) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799293.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578799293 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 20, 32, 32, 40, 40, 40, 20, 20, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 40, 40, 40, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 260 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 514) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799293.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799293.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578799293 none CCC[C@@H](NC(N)=O)C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 38, 19, 38, 38, 42, 42, 42, 19, 19, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 242 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799293 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799293 Building ZINC001578799356 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799356 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 515) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/515 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/515' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799356 none C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 28, 28, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 516) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/516 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/516' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799356 none C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 24, 24, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799356 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 Building ZINC001578799356 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799356 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 515) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799356 none C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 28, 28, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 516) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799356 none C[C@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 24, 24, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799356 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799356 Building ZINC001578799357 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799357 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 517) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/517 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/517' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799357 none C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 25, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 518) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/518 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/518' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799357 none C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 28, 28, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799357 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 Building ZINC001578799357 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799357 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 517) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799357 none C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 25, 25, 10, 10, 10, 10, 3, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 518) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799357 none C[C@@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 28, 28, 11, 11, 11, 11, 3, 11, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 141 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799357 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799357 Building ZINC001578799358 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799358 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 519) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/519 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/519' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799358 none C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 19, 19, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 520) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/520 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/520' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799358 none C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 24, 24, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799358 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 Building ZINC001578799358 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799358 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 519) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799358.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799358 none C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 32, 50, 19, 19, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 520) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799358.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799358.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799358 none C[C@@H]1C[C@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 50, 24, 24, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799358 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799358 Building ZINC001578799359 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799359 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 521) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/521 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/521' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799359 none C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 46, 24, 24, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 522) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/522 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/522' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799359 none C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 48, 19, 19, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799359 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 Building ZINC001578799359 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799359 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 521) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799359.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799359 none C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 35, 46, 24, 24, 9, 9, 9, 9, 3, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 522) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1) `ZINC001578799359.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799359.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799359 none C[C@H]1C[C@@H](C(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)CC(=O)N1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 1, 11, 8, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 33, 48, 19, 19, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 50, 50, 50, 50, 19, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799359 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799359 Building ZINC001578799519 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799519 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 523) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/523 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/523' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1) `ZINC001578799519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799519 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 524) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/524 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/524' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1) `ZINC001578799519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799519 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799519 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 Building ZINC001578799519 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799519 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 523) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/523: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1) `ZINC001578799519.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799519 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 524) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/524: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1) `ZINC001578799519.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799519.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799519 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2ccnc3[nH]nnc32)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', 'N.2', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 8, 1, 8, 6, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 43, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799519 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799519 Building ZINC001578799522 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799522 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 525) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/525 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/525' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1) `ZINC001578799522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799522 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 21, 21, 21, 49, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 43, 43, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 526) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/526 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/526' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1) `ZINC001578799522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799522 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 23, 23, 23, 49, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 23, 42, 42, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799522 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 Building ZINC001578799522 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799522 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 525) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1) `ZINC001578799522.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799522 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 21, 21, 21, 49, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 21, 43, 43, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 526) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1) `ZINC001578799522.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799522.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799522 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 11, 11, 11, 11, 11, 23, 23, 23, 49, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 23, 42, 42, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799522 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799522 Building ZINC001578799523 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799523 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 527) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/527 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/527' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1) `ZINC001578799523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799523 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 45, 45, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 528) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/528 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/528' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1) `ZINC001578799523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799523 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 22, 22, 22, 48, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 43, 43, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799523 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 Building ZINC001578799523 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799523 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 527) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1) `ZINC001578799523.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799523 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 10, 10, 10, 10, 10, 24, 24, 24, 50, 50, 50, 50, 50, 50, 50, 50, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 24, 45, 45, 50, 50, 50, 50, 50, 50, 50, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 177 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 528) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1) `ZINC001578799523.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799523.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001578799523 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)C[C@H]2CCCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 7, 5, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 22, 22, 22, 48, 50, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 22, 43, 43, 50, 50, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799523 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799523 Building ZINC001578799574 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799574 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 529) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/529 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/529' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578799574 none Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 43, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 530) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/530 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/530' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578799574 none Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 43, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799574 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 Building ZINC001578799574 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799574 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 529) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799574.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578799574 none Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 43, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 530) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578799574.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799574.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001578799574 none Cc1nn(C)c(F)c1C(=O)N[C@H]1C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 15, 1, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 14, 14, 14, 14, 4, 14, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 50, 50, 50, 50, 50, 50, 43, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 14] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46]) total number of confs: 132 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799574 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799574 Building ZINC001578799609 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799609 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 531) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/531 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/531' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578799609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799609 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 532) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/532 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/532' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578799609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799609 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799609 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 Building ZINC001578799609 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799609 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 531) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578799609.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799609 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 532) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1) `ZINC001578799609.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799609.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578799609 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)c2cccn3nnnc23)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'N.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 1, 1, 1, 1, 8, 8, 8, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 15, 15, 15, 15, 15, 44, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 15, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 15, 15, 44, 50, 50, 50, 15, 15] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799609 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799609 Building ZINC001578799610 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799610 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 533) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/533 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/533' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001578799610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799610 none CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 17, 17, 17, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 31, 31, 50, 50, 50, 50, 50, 31, 30, 30, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 534) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/534 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/534' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001578799610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799610 none CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 18, 18, 18, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 33, 33, 50, 50, 50, 50, 50, 33, 32, 32, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799610 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 Building ZINC001578799610 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799610 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 533) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/533: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001578799610.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799610 none CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 17, 17, 17, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 31, 31, 50, 50, 50, 50, 50, 31, 30, 30, 17, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 534) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/534: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001578799610.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799610.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001578799610 none CCn1cc(CC(=O)N[C@H]2C[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', '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, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 18, 18, 18, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 33, 33, 50, 50, 50, 50, 50, 33, 32, 32, 18, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799610 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799610 Building ZINC001578799725 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799725 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 535) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/535 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/535' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001578799725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578799725 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 48, 48, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 536) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/536 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/536' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001578799725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578799725 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 48, 48, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799725 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 Building ZINC001578799725 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578799725 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 535) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001578799725.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578799725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578799725 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 48, 48, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 536) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1) `ZINC001578799725.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578799725.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001578799725 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1C[C@@H](NC(=O)CCc2cncnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 8, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 3, 11, 11, 11, 11, 11, 27, 27, 27, 48, 50, 50, 50, 50, 50, 50, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 27, 48, 48, 50, 50, 50, 50, 50, 11, 11] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578799725 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578799725 Building ZINC001578901915 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578901915 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 537) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/537 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/537' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578901915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901915 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 26, 26, 26, 26, 26, 26, 33, 33, 37, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 26, 26, 26, 26, 26, 37, 37, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 538) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/538 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/538' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578901915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901915 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 30, 30, 30, 30, 30, 30, 39, 39, 43, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 30, 30, 30, 30, 30, 30, 43, 43, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578901915 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 Building ZINC001578901915 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578901915 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 537) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901915.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578901915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901915 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 26, 26, 26, 26, 26, 26, 33, 33, 37, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 26, 26, 26, 26, 26, 26, 37, 37, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 151 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 538) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901915.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578901915.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901915 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 30, 30, 30, 30, 30, 30, 39, 39, 43, 50, 50, 50, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 30, 30, 30, 30, 30, 30, 43, 43, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 156 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578901915 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901915 Building ZINC001578901920 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578901920 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 539) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/539 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/539' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901920 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 39, 39, 43, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 29, 29, 29, 29, 29, 43, 43, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 540) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/540 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/540' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901920 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 24, 24, 24, 24, 24, 31, 31, 35, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 24, 24, 24, 24, 24, 35, 35, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 150 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578901920 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 Building ZINC001578901920 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578901920 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 539) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901920.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901920 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 39, 39, 43, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 29, 29, 29, 29, 29, 29, 43, 43, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 159 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 540) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1) `ZINC001578901920.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578901920.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001578901920 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)Cc2nc[nH]n2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'N.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 1, 8, 1, 8, 6, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 24, 24, 24, 24, 24, 24, 31, 31, 35, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 24, 24, 24, 24, 24, 24, 35, 35, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 150 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578901920 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578901920 Building ZINC001578902070 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578902070 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 541) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/541 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/541' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578902070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902070 none Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 48, 44, 44, 44, 44, 22, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 542) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/542 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/542' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578902070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902070 none Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 48, 42, 42, 42, 42, 18, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578902070 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 Building ZINC001578902070 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578902070 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 541) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902070.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578902070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902070 none Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 48, 44, 44, 44, 44, 22, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 137 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 542) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902070.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578902070.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902070 none Cc1c(C(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 48, 42, 42, 42, 42, 18, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578902070 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902070 Building ZINC001578902077 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578902077 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 543) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/543 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/543' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578902077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902077 none Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 48, 42, 42, 42, 42, 18, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 544) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/544 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/544' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578902077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902077 none Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 48, 44, 44, 44, 44, 21, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578902077 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 Building ZINC001578902077 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578902077 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 543) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902077.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578902077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902077 none Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 42, 48, 42, 42, 42, 42, 18, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 42, 42, 42, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 544) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C) `ZINC001578902077.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578902077.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001578902077 none Cc1c(C(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nnn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 44, 48, 44, 44, 44, 44, 21, 44, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 44, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 44, 44, 44, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 44, 44, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 132 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578902077 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578902077 Building ZINC001578903682 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903682 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 545) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/545 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/545' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 28, 28, 28, 28, 28, 28, 36, 36, 42, 44, 47, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 28, 28, 28, 28, 28, 42, 42, 44, 44, 47, 47, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 546) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/546 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/546' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 29, 29, 29, 40, 40, 46, 46, 48, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 46, 46, 46, 46, 48, 48, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903682 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 Building ZINC001578903682 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903682 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 545) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903682.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903682 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 28, 28, 28, 28, 28, 28, 36, 36, 42, 44, 47, 50, 50, 28, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 28, 28, 28, 28, 28, 28, 42, 42, 44, 44, 47, 47, 50, 50, 28, 28] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 192 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 546) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903682.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903682.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903682 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 29, 29, 29, 29, 29, 29, 40, 40, 46, 46, 48, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 29, 29, 29, 29, 29, 29, 46, 46, 46, 46, 48, 48, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 12 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903682 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903682 Building ZINC001578903684 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903684 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 547) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/547 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/547' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903684 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 46, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 46, 46, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 548) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/548 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/548' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903684 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 30, 30, 30, 30, 30, 30, 31, 31, 31, 31, 43, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 30, 30, 30, 30, 30, 30, 31, 31, 31, 31, 43, 43, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903684 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 Building ZINC001578903684 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903684 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 547) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903684.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903684 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 46, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 46, 46, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 548) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1) `ZINC001578903684.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903684.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578903684 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)CCCC(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 20, 30, 30, 30, 30, 30, 30, 31, 31, 31, 31, 43, 50, 50, 30, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 14, 14, 30, 30, 30, 30, 30, 30, 31, 31, 31, 31, 43, 43, 50, 50, 30, 30] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903684 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903684 Building ZINC001578903823 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903823 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 549) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/549 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/549' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903823 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 31, 31, 31, 31, 39, 39, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 550) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/550 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/550' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903823 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 34, 34, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903823 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 Building ZINC001578903823 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903823 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 549) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903823.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903823 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 31, 31, 31, 31, 39, 39, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 550) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903823.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903823.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903823 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 16, 29, 29, 29, 29, 29, 29, 34, 34, 50, 50, 50, 50, 50, 29, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 29, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 29, 29] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903823 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903823 Building ZINC001578903824 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903824 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 551) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/551 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/551' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903824 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 31, 31, 31, 31, 41, 41, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 552) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/552 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/552' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903824 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 31, 31, 31, 31, 41, 41, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903824 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 Building ZINC001578903824 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578903824 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 551) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/551: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903824.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578903824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903824 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 31, 31, 31, 31, 41, 41, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 552) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/552: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1) `ZINC001578903824.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578903824.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001578903824 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCCN(C(=O)C2=COCCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 1, 12, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 17, 31, 31, 31, 31, 31, 31, 41, 41, 50, 50, 50, 50, 50, 31, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 11, 11, 31, 31, 31, 31, 31, 31, 50, 50, 50, 50, 50, 31, 31] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578903824 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578903824 Building ZINC001578904686 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578904686 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 553) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/553 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/553' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578904686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904686 none CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 26, 23, 26, 23, 23, 23, 23, 16, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 31, 29, 29, 23, 23, 23, 23, 23, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 219 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 554) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/554 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/554' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578904686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904686 none CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 33, 29, 28, 29, 28, 28, 28, 28, 18, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 33, 31, 31, 28, 28, 28, 28, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578904686 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 Building ZINC001578904686 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578904686 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 553) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578904686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904686 none CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 31, 31, 29, 31, 26, 23, 26, 23, 23, 23, 23, 16, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 31, 29, 29, 23, 23, 23, 23, 23, 23, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 219 number of broken/clashed sets: 8 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 554) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578904686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904686 none CCNC(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 31, 33, 29, 28, 29, 28, 28, 28, 28, 18, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 33, 31, 31, 28, 28, 28, 28, 28, 28, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578904686 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904686 Building ZINC001578904687 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578904687 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 555) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/555 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/555' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578904687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904687 none CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 33, 28, 27, 28, 27, 27, 27, 27, 18, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 33, 30, 30, 27, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 556) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/556 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/556' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578904687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904687 none CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 31, 24, 22, 24, 22, 22, 22, 22, 16, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 31, 28, 28, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 221 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578904687 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 Building ZINC001578904687 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578904687 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 555) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578904687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904687 none CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 30, 33, 28, 27, 28, 27, 27, 27, 27, 18, 27, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 33, 30, 30, 27, 27, 27, 27, 27, 27, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 27] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 205 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 556) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578904687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578904687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578904687 none CCNC(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 28, 31, 24, 22, 24, 22, 22, 22, 22, 16, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 31, 28, 28, 22, 22, 22, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 221 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578904687 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578904687 Building ZINC001578905560 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905560 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 557) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/557 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/557' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905560 none CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 34, 29, 34, 29, 29, 29, 29, 17, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 49, 49, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 558) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/558 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/558' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905560 none CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 50, 29, 20, 29, 20, 20, 20, 20, 14, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 45, 45, 20, 20, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 191 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905560 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 Building ZINC001578905560 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905560 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 557) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905560.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905560 none CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 49, 50, 34, 29, 34, 29, 29, 29, 29, 17, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 49, 49, 29, 29, 29, 29, 29, 29, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 558) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905560.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905560.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905560 none CN(C)C(=O)CC(=O)N1CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 50, 29, 20, 29, 20, 20, 20, 20, 14, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 20, 50, 50, 50, 50, 50, 50, 45, 45, 20, 20, 20, 20, 20, 20, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 20] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 191 number of broken/clashed sets: 23 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905560 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905560 Building ZINC001578905561 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905561 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 559) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/559 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/559' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905561 none CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 50, 28, 19, 28, 19, 19, 19, 19, 13, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 45, 45, 19, 19, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 560) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/560 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/560' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905561 none CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 28, 34, 28, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 193 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905561 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 Building ZINC001578905561 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905561 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 559) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905561.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905561 none CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 50, 28, 19, 28, 19, 19, 19, 19, 13, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 50, 50, 50, 50, 50, 50, 45, 45, 19, 19, 19, 19, 19, 19, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 19] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 24 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 560) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578905561.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905561.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905561 none CN(C)C(=O)CC(=O)N1CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 28, 34, 28, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 28, 28, 28, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 193 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905561 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905561 Building ZINC001578905805 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905805 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 561) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/561 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/561' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905805 none Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 33, 23, 33, 23, 23, 23, 23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 47, 47, 23, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 562) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/562 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/562' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905805 none Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 32, 21, 32, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 47, 47, 21, 21, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905805 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 Building ZINC001578905805 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905805 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 561) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905805.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905805 none Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 33, 23, 33, 23, 23, 23, 23, 12, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 47, 47, 23, 23, 23, 23, 23, 23, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 186 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 562) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905805.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905805.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905805 none Cn1cc(CC(=O)N2CCC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 32, 21, 32, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 47, 47, 21, 21, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 182 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905805 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905805 Building ZINC001578905807 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905807 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 563) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/563 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/563' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905807 none Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 33, 21, 33, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 47, 47, 21, 21, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 564) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/564 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/564' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905807 none Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 34, 24, 34, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 47, 47, 24, 24, 24, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905807 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 Building ZINC001578905807 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578905807 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 563) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905807.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578905807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905807 none Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 33, 21, 33, 21, 21, 21, 21, 13, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 47, 47, 21, 21, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 178 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 564) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1) `ZINC001578905807.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578905807.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001578905807 none Cn1cc(CC(=O)N2CCC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)cn1 NO_LONG_NAME dock atom types: ['C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 1, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 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, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 47, 34, 24, 34, 24, 24, 24, 24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 47, 47, 24, 24, 24, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24, 50] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52]) total number of confs: 184 number of broken/clashed sets: 20 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578905807 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578905807 Building ZINC001578918282 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578918282 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 565) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/565 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/565' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578918282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918282 none C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 33, 33, 14, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 33, 14, 14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 566) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/566 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/566' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578918282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918282 none C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 50, 50, 50, 50, 29, 29, 10, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 29, 10, 10, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578918282 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 Building ZINC001578918282 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578918282 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 565) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918282.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578918282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918282 none C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 33, 33, 14, 5, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 33, 14, 14, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 566) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918282.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578918282.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918282 none C[C@H](NC(N)=O)C(=O)NC[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 29, 50, 50, 50, 50, 50, 29, 29, 10, 3, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 50, 50, 50, 50, 50, 50, 29, 10, 10, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578918282 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918282 Building ZINC001578918283 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578918283 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 567) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/567 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/567' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578918283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918283 none C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 50, 50, 50, 50, 50, 26, 26, 11, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 26, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 568) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/568 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/568' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578918283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918283 none C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 50, 50, 50, 32, 32, 13, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 50, 50, 50, 32, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578918283 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 Building ZINC001578918283 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001578918283 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 567) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918283.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001578918283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918283 none C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 26, 50, 50, 50, 50, 50, 26, 26, 11, 5, 5, 5, 5, 5, 5, 5, 2, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 26, 11, 11, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 568) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001578918283.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001578918283.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001578918283 none C[C@H](NC(N)=O)C(=O)NC[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 4, 7, 4, 6, 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, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 49, 49, 50, 50, 50, 32, 32, 13, 4, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 49, 49, 49, 50, 50, 50, 32, 13, 13, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001578918283 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001578918283 Building ZINC001579050100 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050100 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 569) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/569 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/569' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050100 none CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 38, 31, 38, 31, 31, 31, 31, 9, 31, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 44, 44, 31, 31, 31, 31, 31, 31, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 570) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/570 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/570' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050100 none CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 37, 22, 37, 22, 22, 22, 22, 6, 22, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 43, 43, 22, 22, 22, 22, 22, 22, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050100 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 Building ZINC001579050100 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050100 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 569) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/569: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050100.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050100 none CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 38, 31, 38, 31, 31, 31, 31, 9, 31, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 44, 44, 31, 31, 31, 31, 31, 31, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 570) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/570: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050100.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050100.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050100 none CC(=O)NCC(=O)N1CCC[C@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 43, 37, 22, 37, 22, 22, 22, 22, 6, 22, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 43, 43, 22, 22, 22, 22, 22, 22, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 171 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050100 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050100 Building ZINC001579050101 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050101 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 571) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/571 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/571' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050101 none CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 36, 21, 36, 21, 21, 21, 21, 6, 21, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 42, 42, 21, 21, 21, 21, 21, 21, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 572) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/572 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/572' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050101 none CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 38, 31, 38, 31, 31, 31, 31, 9, 31, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 44, 44, 31, 31, 31, 31, 31, 31, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050101 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 Building ZINC001579050101 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050101 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 571) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050101.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050101 none CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 36, 21, 36, 21, 21, 21, 21, 6, 21, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 42, 42, 21, 21, 21, 21, 21, 21, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 572) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050101.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050101.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050101 none CC(=O)NCC(=O)N1CCC[C@@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 44, 38, 31, 38, 31, 31, 31, 31, 9, 31, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 44, 44, 31, 31, 31, 31, 31, 31, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 31] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 166 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050101 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050101 Building ZINC001579050103 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050103 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 573) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/573 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/573' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050103 none CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 29, 23, 29, 23, 23, 23, 23, 8, 23, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 42, 42, 23, 23, 23, 23, 23, 23, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 574) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/574 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/574' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050103 none CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 31, 22, 31, 22, 22, 22, 22, 6, 22, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 45, 45, 22, 22, 22, 22, 22, 22, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050103 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 Building ZINC001579050103 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050103 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 573) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050103 none CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 29, 23, 29, 23, 23, 23, 23, 8, 23, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 42, 42, 23, 23, 23, 23, 23, 23, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 574) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050103 none CC(=O)NCC(=O)N1CCC[C@@H]([C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 31, 22, 31, 22, 22, 22, 22, 6, 22, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 45, 45, 22, 22, 22, 22, 22, 22, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 22] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 183 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050103 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050103 Building ZINC001579050104 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050104 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 575) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/575 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/575' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050104 none CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 30, 21, 30, 21, 21, 21, 21, 6, 21, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 45, 45, 21, 21, 21, 21, 21, 21, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 179 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 576) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/576 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/576' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050104 none CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 29, 23, 29, 23, 23, 23, 23, 8, 23, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 42, 42, 23, 23, 23, 23, 23, 23, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050104 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 Building ZINC001579050104 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579050104 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 575) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050104.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579050104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050104 none CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 45, 30, 21, 30, 21, 21, 21, 21, 6, 21, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 45, 45, 21, 21, 21, 21, 21, 21, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 179 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 576) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001579050104.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579050104.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579050104 none CC(=O)NCC(=O)N1CCC[C@H]([C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 4, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 42, 29, 23, 29, 23, 23, 23, 23, 8, 23, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 42, 42, 23, 23, 23, 23, 23, 23, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 23] 50 rigid atoms, others: [49, 42, 43, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 190 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579050104 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579050104 Building ZINC001579113120 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113120 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 577) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/577 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/577' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001579113120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113120 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 18, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 578) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/578 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/578' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001579113120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113120 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 20, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113120 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 Building ZINC001579113120 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113120 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 577) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001579113120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113120 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 8, 18, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 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/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 578) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C) `ZINC001579113120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113120 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 9, 20, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48]) total number of confs: 100 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113120 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113120 Building ZINC001579113139 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113139 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 579) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/579 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/579' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21) `ZINC001579113139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 25, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 580) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/580 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/580' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21) `ZINC001579113139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 25, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113139 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 Building ZINC001579113139 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113139 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 579) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21) `ZINC001579113139.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113139 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 6, 6, 6, 6, 17, 25, 50, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 6, 6, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 580) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21) `ZINC001579113139.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113139.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113139 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)C3(C)CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 7, 7, 17, 25, 50, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 7, 7, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 147 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113139 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113139 Building ZINC001579113440 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113440 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 581) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/581 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/581' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113440 none Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 582) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/582 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/582' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113440 none Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 11, 7, 11, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113440 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 Building ZINC001579113440 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113440 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 581) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113440.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113440 none Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 582) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113440.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113440.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113440 none Cc1nccn1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 34, 11, 7, 11, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 34, 34, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113440 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113440 Building ZINC001579113470 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113470 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 583) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/583 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/583' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113470 none CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 42, 42, 23, 7, 23, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 42, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 584) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/584 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/584' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113470 none CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 26, 9, 26, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 39, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113470 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 Building ZINC001579113470 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113470 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 583) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113470.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113470 none CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 42, 42, 42, 42, 42, 23, 7, 23, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 42, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 584) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113470.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113470.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113470 none CCn1nncc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 26, 9, 26, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 39, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113470 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113470 Building ZINC001579113495 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113495 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 585) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/585 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/585' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001579113495 none CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 36, 32, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 37, 37, 32, 32, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 586) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/586 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/586' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001579113495 none CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 35, 31, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 36, 36, 31, 31, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113495 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 Building ZINC001579113495 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113495 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 585) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/585: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113495.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001579113495 none CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 39, 36, 32, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 39, 39, 37, 37, 32, 32, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 586) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/586: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113495.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113495.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 58 natoms 57 natoms 56 natoms 55 names: ZINC001579113495 none CN(C)CCCCC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 38, 35, 31, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 38, 38, 36, 36, 31, 31, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 54, 46, 47, 48, 49, 50, 19, 52, 21, 22, 23, 24, 25, 26, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 220 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113495 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113495 Building ZINC001579113498 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113498 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 587) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/587 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/587' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001579113498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113498 none COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 8, 16, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 588) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/588 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/588' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001579113498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113498 none COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113498 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 Building ZINC001579113498 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113498 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 587) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001579113498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113498 none COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 16, 8, 16, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 95 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 588) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1) `ZINC001579113498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113498 none COc1ccnc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 13, 7, 13, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113498 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113498 Building ZINC001579113501 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113501 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 589) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/589 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/589' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001579113501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113501 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 590) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/590 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/590' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001579113501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113501 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113501 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 Building ZINC001579113501 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113501 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 589) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001579113501.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113501 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 590) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001579113501.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113501.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113501 none COc1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46]) total number of confs: 105 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113501 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113501 Building ZINC001579113538 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113538 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 591) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/591 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/591' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21) `ZINC001579113538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113538 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 6, 26, 23, 43, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 26, 26, 29, 29, 40, 40, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 592) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/592 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/592' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21) `ZINC001579113538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113538 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 6, 25, 24, 43, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 29, 29, 40, 39, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113538 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 Building ZINC001579113538 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113538 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 591) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/591: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21) `ZINC001579113538.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113538 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 6, 6, 26, 23, 43, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 26, 26, 29, 29, 40, 40, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 219 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 592) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/592: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21) `ZINC001579113538.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113538.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113538 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3cccn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 8, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 5, 5, 6, 6, 25, 24, 43, 50, 50, 50, 50, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 25, 25, 29, 29, 40, 39, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113538 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113538 Building ZINC001579113554 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113554 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 593) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/593 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/593' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579113554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113554 none Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 25, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 29, 29, 25, 25, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 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/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 594) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/594 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/594' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579113554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113554 none Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 27, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 30, 30, 27, 27, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 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/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113554 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 Building ZINC001579113554 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113554 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 593) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579113554.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113554 none Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 29, 25, 9, 6, 9, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 29, 29, 25, 25, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 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/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 594) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579113554.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113554.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001579113554 none Cc1noc(CCC(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 27, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 30, 30, 27, 27, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 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/167320/xcr-8058097.70/working/building/ZINC001579113554 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113554 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113554 Building ZINC001579113626 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113626 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 595) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/595 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/595' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21) `ZINC001579113626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113626 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 21, 20, 27, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 26, 26, 27, 27, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 596) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/596 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/596' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21) `ZINC001579113626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113626 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 21, 21, 28, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 27, 27, 28, 28, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113626 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 Building ZINC001579113626 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113626 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 595) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21) `ZINC001579113626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113626 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 21, 20, 27, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 26, 26, 27, 27, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 596) grep: /scratch/xiaobo/167320/xcr-8058097.70/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)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21) `ZINC001579113626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579113626 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCCn3ccnc3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 8, 1, 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] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 4, 4, 5, 5, 21, 21, 28, 50, 50, 50, 50, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 21, 21, 27, 27, 28, 28, 50, 50, 50, 4, 4] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 37, 35, 7, 36, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113626 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113626 Building ZINC001579113629 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113629 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 597) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/597 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/597' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001579113629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113629 none CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 19, 9, 19, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 38, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 598) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/598 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/598' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001579113629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113629 none CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 10, 21, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113629 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 Building ZINC001579113629 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113629 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 597) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001579113629.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113629 none CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 19, 9, 19, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 38, 38, 50, 50, 50, 50, 50, 38, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 598) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001579113629.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113629.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579113629 none CCn1cc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 21, 10, 21, 10, 10, 10, 10, 10, 10, 10, 2, 10, 2, 1, 2, 1, 1, 1, 1, 1, 1, 43, 43, 50, 50, 50, 50, 50, 43, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113629 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113629 Building ZINC001579113746 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113746 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 599) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/599 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/599' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21) `ZINC001579113746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113746 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 11, 11, 39, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 600) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/600 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/600' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21) `ZINC001579113746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113746 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 10, 10, 41, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113746 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 Building ZINC001579113746 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113746 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 599) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/599: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21) `ZINC001579113746.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113746 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 11, 11, 39, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 600) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/600: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21) `ZINC001579113746.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113746.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579113746 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CC3CCOCC3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 5, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 10, 10, 41, 50, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 31, 31, 50, 50, 50, 50, 50, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113746 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113746 Building ZINC001579113791 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113791 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 601) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/601 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/601' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113791 none CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 41, 41, 41, 22, 7, 22, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 602) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/602 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/602' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113791 none CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113791 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 Building ZINC001579113791 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113791 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 601) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579113791.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113791 none CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 41, 41, 41, 41, 41, 41, 22, 7, 22, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 41, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 148 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 602) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579113791.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113791.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113791 none CCc1nc[nH]c1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 1, 8, 1, 8, 6, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 7, 7, 4, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 43, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 144 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113791 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113791 Building ZINC001579113806 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113806 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 603) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/603 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/603' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001579113806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579113806 none COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 50, 50, 50, 27, 9, 27, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 604) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/604 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/604' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001579113806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579113806 none COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113806 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 Building ZINC001579113806 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113806 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 603) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001579113806.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579113806 none COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 50, 50, 50, 27, 9, 27, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 604) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1) `ZINC001579113806.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113806.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579113806 none COc1nc(C(=O)N2C[C@H]3[C@@H](C2)[C@@H]3NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 8, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 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, 50, 50, 50, 24, 9, 24, 9, 9, 9, 9, 9, 9, 9, 2, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 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/167320/xcr-8058097.70/working/building/ZINC001579113806 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113806 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113806 Building ZINC001579113832 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113832 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 605) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/605 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/605' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21) `ZINC001579113832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113832 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 6, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 12, 12, 36, 46, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 36, 36, 46, 46, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 606) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/606 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/606' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21) `ZINC001579113832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113832 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 6, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 11, 11, 37, 47, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 37, 37, 47, 47, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113832 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 Building ZINC001579113832 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579113832 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 605) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/605: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21) `ZINC001579113832.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579113832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113832 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 6, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 12, 12, 36, 46, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 36, 36, 46, 46, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 606) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/606: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21) `ZINC001579113832.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579113832.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579113832 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)CCc3ncc[nH]3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 5, 1, 8, 1, 1, 8, 6, 5, 5, 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, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 11, 11, 37, 47, 50, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 37, 37, 47, 47, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 36, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579113832 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579113832 Building ZINC001579114082 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114082 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 607) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/607 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/607' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114082 none C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 7, 17, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 31, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 608) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/608 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/608' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114082 none C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 8, 18, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 32, 32, 32, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114082 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 Building ZINC001579114082 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114082 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 607) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/607: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114082.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114082 none C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 7, 17, 7, 7, 7, 7, 7, 7, 7, 2, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 31, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 156 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 608) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/608: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114082.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114082.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114082 none C[C@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 18, 32, 8, 18, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 32, 32, 32, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114082 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114082 Building ZINC001579114083 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114083 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 609) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/609 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/609' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114083 none C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 29, 6, 14, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 29, 29, 29, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 610) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/610 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/610' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114083 none C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 16, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114083 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 Building ZINC001579114083 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114083 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 609) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114083.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114083 none C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 29, 6, 14, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 29, 29, 29, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 610) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1) `ZINC001579114083.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114083.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579114083 none C[C@@H](C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 1, 8, 8, 5, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 16, 8, 8, 8, 8, 8, 8, 8, 2, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 50, 50, 50, 50, 50, 31, 31, 31, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114083 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114083 Building ZINC001579114345 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114345 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 611) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/611 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/611' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21) `ZINC001579114345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001579114345 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 11, 11, 30, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 30, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 612) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/612 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/612' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21) `ZINC001579114345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001579114345 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 11, 11, 35, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 35, 35, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114345 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 Building ZINC001579114345 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114345 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 611) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/611: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21) `ZINC001579114345.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001579114345 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 6, 6, 6, 6, 6, 6, 11, 11, 30, 50, 50, 50, 50, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 6, 6, 30, 30, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 612) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/612: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21) `ZINC001579114345.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114345.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 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: ZINC001579114345 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@@H]1[C@H]2CN(C(=O)Cc3cscn3)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'C.2', 'S.3', 'C.2', 'N.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 1, 1, 14, 1, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 7, 7, 7, 7, 7, 7, 11, 11, 35, 50, 50, 50, 50, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 7, 7, 35, 35, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114345 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114345 Building ZINC001579114354 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114354 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 613) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/613 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/613' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579114354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579114354 none Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 12, 32, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 614) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/614 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/614' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579114354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579114354 none Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 11, 32, 11, 11, 11, 11, 11, 11, 11, 4, 11, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114354 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 Building ZINC001579114354 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114354 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 613) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579114354.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579114354 none Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 12, 32, 12, 12, 12, 12, 12, 12, 12, 4, 12, 4, 1, 4, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 20, 22, 23, 24, 25, 26, 27] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 614) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579114354.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114354.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 22 is the cov attach 4 22 0 4 22 1 4 22 2 3 22 2 25 to be deleted 26 to be deleted 27 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579114354 none Cn1c(=O)cccc1C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 32, 11, 32, 11, 11, 11, 11, 11, 11, 11, 4, 11, 4, 1, 4, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 50, 11, 11, 11, 11, 4, 2, 2, 2, 2, 2, 2, 2, 2, 2] 50 rigid atoms, others: [24, 20, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 27, 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/167320/xcr-8058097.70/working/building/ZINC001579114354 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114354 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114354 Building ZINC001579114419 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114419 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 615) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/615 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/615' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579114419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579114419 none Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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, 45, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 45, 45, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 616) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/616 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/616' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579114419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579114419 none Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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, 41, 13, 6, 13, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 41, 41, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114419 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 Building ZINC001579114419 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579114419 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 615) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579114419.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579114419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579114419 none Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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, 45, 11, 6, 11, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 45, 45, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 616) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579114419.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579114419.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579114419 none Cc1nonc1CC(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'N.2', 'C.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 8, 1, 5, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 12, 5, 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, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 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, 41, 13, 6, 13, 6, 6, 6, 6, 6, 6, 6, 2, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 41, 41, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579114419 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579114419 Building ZINC001579115383 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579115383 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 617) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/617 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/617' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001579115383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579115383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001579115383 none CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.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, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 0 hydrogens 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, 24, 24, 9, 24, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 24, 24, 24, 24, 24, 5, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 618) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/618 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/618' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001579115383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579115383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001579115383 none CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.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, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 23, 23, 23, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 32, 32, 32, 23, 23, 23, 23, 23, 4, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579115383 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 Building ZINC001579115383 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579115383 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 617) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001579115383.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579115383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001579115383 none CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.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, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 0 hydrogens 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, 24, 24, 9, 24, 5, 1, 5, 1, 1, 1, 11, 11, 11, 11, 11, 30, 30, 30, 24, 24, 24, 24, 24, 5, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 618) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001579115383.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579115383.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001579115383 none CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.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, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 1, 1, 17, 14, 7, 7, 7, 7, 7, 6, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 23, 23, 23, 23, 23, 23, 8, 23, 4, 1, 4, 1, 1, 1, 11, 11, 11, 11, 11, 32, 32, 32, 23, 23, 23, 23, 23, 4, 11, 11] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 88 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579115383 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115383 Building ZINC001579115781 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579115781 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 619) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/619 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/619' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001579115781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579115781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001579115781 none CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 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: [23, 16, 16, 16, 16, 16, 16, 5, 16, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 23, 23, 23, 16, 16, 16, 16, 16, 5, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 620) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/620 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/620' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001579115781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579115781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001579115781 none CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 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, 19, 19, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 25, 25, 25, 19, 19, 19, 19, 19, 5, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579115781 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 Building ZINC001579115781 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579115781 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 619) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/619: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001579115781.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579115781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001579115781 none CO[C@@H]1CNC[C@H]1NC(=O)[C@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 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: [23, 16, 16, 16, 16, 16, 16, 5, 16, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 7, 11, 11, 4, 4, 23, 23, 23, 16, 16, 16, 16, 16, 5, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 77 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 620) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/620: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C) `ZINC001579115781.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579115781.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001579115781 none CO[C@@H]1CNC[C@H]1NC(=O)[C@@]([O-])([SiH3])c1c(C)nn(c2ccccc2)c1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'C.3', 'N.2', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 5, 10, 5, 5, 7, 8, 1, 11, 5, 12, 1, 1, 5, 8, 8, 1, 1, 1, 1, 1, 1, 1, 5, 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, 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, 19, 19, 19, 19, 19, 19, 5, 19, 5, 1, 5, 1, 1, 1, 4, 4, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 25, 25, 25, 19, 19, 19, 19, 19, 5, 4, 4, 4, 11, 11, 8, 11, 11, 4, 4, 4] 50 rigid atoms, others: [10, 12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 82 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579115781 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579115781 Building ZINC001579130113 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579130113 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 621) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/621 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/621' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1) `ZINC001579130113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579130113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130113 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 40, 50, 50, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 40, 40, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 362 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 622) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/622 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/622' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1) `ZINC001579130113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579130113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130113 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 38, 49, 50, 48, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 38, 38, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 373 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579130113 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 Building ZINC001579130113 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579130113 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 621) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1) `ZINC001579130113.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579130113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130113 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 18, 18, 18, 40, 50, 50, 49, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 18, 40, 40, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 362 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 622) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1) `ZINC001579130113.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579130113.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130113 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 16, 16, 16, 38, 49, 50, 48, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 16, 38, 38, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 373 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579130113 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130113 Building ZINC001579130115 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579130115 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 623) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/623 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/623' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1) `ZINC001579130115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579130115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130115 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 44, 42, 50, 48, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 44, 44, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 408 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 624) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/624 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/624' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1) `ZINC001579130115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579130115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130115 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 42, 44, 50, 48, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 42, 42, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 393 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579130115 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 Building ZINC001579130115 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579130115 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 623) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1) `ZINC001579130115.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579130115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130115 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 16, 16, 16, 44, 42, 50, 48, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 16, 44, 44, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 408 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 624) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1) `ZINC001579130115.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579130115.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579130115 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)C[C@](C)(O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 5, 12, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 1, 1, 1, 1, 1, 3, 3, 5, 5, 5, 5, 5, 5, 5, 5, 5, 17, 17, 17, 42, 44, 50, 48, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 17, 42, 42, 50, 50, 50, 150, 50, 50, 50, 50, 50] 150 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 393 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579130115 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579130115 Building ZINC001579146665 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579146665 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 625) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/625 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/625' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579146665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579146665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579146665 none CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 7, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 29, 29, 29, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 626) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/626 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/626' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579146665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579146665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579146665 none CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 7, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 29, 29, 29, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579146665 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 Building ZINC001579146665 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579146665 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 625) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/625: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579146665.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579146665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579146665 none CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 7, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 29, 29, 29, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 626) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/626: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579146665.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579146665.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579146665 none CN(CCN(C)c1ccc(c2nn[nH]n2)nc1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'N.ar', 'C.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 5, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 8, 1, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 3, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 2, 3, 7, 7, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 3, 3, 3, 7, 7, 7, 7, 29, 29, 29, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 124 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579146665 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579146665 Building ZINC001579159843 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579159843 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 627) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/627 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/627' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1) `ZINC001579159843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579159843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001579159843 none Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 41, 12, 12, 12, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 41, 41, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 628) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/628 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/628' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1) `ZINC001579159843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579159843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001579159843 none Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 40, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 50, 50, 50, 50, 50, 47, 47, 40, 40, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579159843 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 Building ZINC001579159843 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579159843 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 627) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1) `ZINC001579159843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579159843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001579159843 none Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 48, 41, 12, 12, 12, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 50, 50, 50, 50, 50, 48, 48, 41, 41, 12, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 628) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1) `ZINC001579159843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579159843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 54 natoms 53 natoms 52 natoms 51 names: ZINC001579159843 none Cc1cnn(CCC(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 8, 8, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 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, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 47, 40, 12, 12, 12, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 50, 50, 50, 50, 50, 47, 47, 40, 40, 12, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579159843 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579159843 Building ZINC001579160349 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579160349 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 629) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/629 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/629' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1) `ZINC001579160349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579160349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001579160349 none CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 29, 29, 50, 50, 26, 26, 26, 20, 20, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 630) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/630 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/630' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1) `ZINC001579160349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579160349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001579160349 none CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 30, 33, 33, 50, 50, 30, 30, 30, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579160349 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 Building ZINC001579160349 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579160349 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 629) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/629: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1) `ZINC001579160349.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579160349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001579160349 none CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 8, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 26, 29, 29, 50, 50, 26, 26, 26, 20, 20, 8, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 630) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/630: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1) `ZINC001579160349.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579160349.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 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: ZINC001579160349 none CN(CC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C(=O)C1CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 1, 11, 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, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 7, 7, 3, 3, 3, 3, 3, 3, 3, 1, 3, 1, 1, 1, 1, 1, 1, 3, 3, 3, 30, 33, 33, 50, 50, 30, 30, 30, 24, 24, 7, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 50, 50, 50, 50, 50] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 12, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579160349 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579160349 Building ZINC001579168400 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579168400 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 631) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/631 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/631' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001579168400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579168400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579168400 none COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 37, 26, 23, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 46, 46, 26, 26, 23, 23, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 632) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/632 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/632' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001579168400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579168400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579168400 none COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 35, 26, 22, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 46, 46, 26, 26, 22, 22, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579168400 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 Building ZINC001579168400 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579168400 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 631) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001579168400.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579168400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579168400 none COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 37, 26, 23, 6, 6, 6, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 46, 46, 26, 26, 23, 23, 6, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 632) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21) `ZINC001579168400.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579168400.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579168400 none COCCOCCC(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 35, 26, 22, 5, 5, 5, 2, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 50, 50, 50, 50, 50, 46, 46, 26, 26, 22, 22, 5, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579168400 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579168400 Building ZINC001579173119 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579173119 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 633) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/633 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/633' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1) `ZINC001579173119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579173119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579173119 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 39, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 12, 39, 39, 46, 46, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 634) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/634 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/634' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1) `ZINC001579173119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579173119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579173119 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 43, 49, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 43, 43, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579173119 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 Building ZINC001579173119 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579173119 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 633) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1) `ZINC001579173119.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579173119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579173119 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 39, 46, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 12, 39, 39, 46, 46, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 634) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1) `ZINC001579173119.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579173119.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001579173119 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCc1ccon1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.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, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 1, 1, 1, 12, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 43, 49, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 14, 43, 43, 49, 49, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579173119 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579173119 Building ZINC001579178110 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579178110 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 635) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/635 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/635' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1) `ZINC001579178110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579178110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579178110 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 27, 29, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 27, 27, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 636) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/636 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/636' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1) `ZINC001579178110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579178110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579178110 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 29, 31, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 29, 29, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579178110 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 Building ZINC001579178110 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579178110 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 635) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1) `ZINC001579178110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579178110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579178110 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 27, 29, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 3, 13, 27, 27, 29, 29, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 150 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 636) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1) `ZINC001579178110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579178110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579178110 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1C[C@H]2[C@@H](C1)[C@@H]2NC(=O)CCn1ccnc1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 7, 5, 5, 7, 8, 1, 11, 5, 5, 8, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 3, 4, 4, 4, 4, 4, 4, 4, 4, 4, 12, 12, 12, 29, 31, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 4, 4, 12, 29, 29, 31, 31, 50, 50, 50] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579178110 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178110 Building ZINC001579178243 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579178243 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 637) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/637 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/637' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579178243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178243 none CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 36, 15, 15, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 36, 50, 50, 50, 36, 36, 36, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 638) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/638 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/638' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579178243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178243 none CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 37, 50, 50, 50, 37, 37, 37, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579178243 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 Building ZINC001579178243 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579178243 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 637) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178243.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579178243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178243 none CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 36, 15, 15, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 36, 50, 50, 50, 36, 36, 36, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 638) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178243.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579178243.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178243 none CO[C@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [37, 37, 17, 37, 17, 17, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 37, 50, 50, 50, 37, 37, 37, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 165 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579178243 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178243 Building ZINC001579178244 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579178244 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 639) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/639 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/639' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579178244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178244 none CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 15, 37, 15, 15, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 39, 50, 50, 50, 38, 38, 38, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 640) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/640 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/640' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579178244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178244 none CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 37, 19, 19, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 37, 50, 50, 50, 37, 37, 37, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579178244 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 Building ZINC001579178244 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579178244 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 639) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178244.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579178244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178244 none CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 37, 15, 37, 15, 15, 5, 5, 5, 5, 5, 5, 3, 1, 3, 1, 1, 1, 1, 1, 1, 5, 5, 5, 39, 50, 50, 50, 38, 38, 38, 15, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 640) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1) `ZINC001579178244.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579178244.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001579178244 none CO[C@@H](C(=O)N[C@@H]1[C@H]2CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]21)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 7, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 19, 37, 19, 19, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 37, 50, 50, 50, 37, 37, 37, 19, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 38, 39, 40, 41, 42, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579178244 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579178244 Building ZINC001579182621 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579182621 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 641) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/641 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/641' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1) `ZINC001579182621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579182621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579182621 none CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 21, 13, 13, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 43, 43, 43, 50, 50, 50, 50, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 642) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/642 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/642' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1) `ZINC001579182621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579182621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579182621 none CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 17, 17, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 46, 46, 46, 50, 50, 50, 50, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579182621 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 Building ZINC001579182621 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579182621 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 641) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1) `ZINC001579182621.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579182621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579182621 none CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 43, 50, 21, 13, 13, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 43, 43, 43, 50, 50, 50, 50, 13, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 43, 43, 43, 43, 43, 43] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 149 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 642) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1) `ZINC001579182621.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579182621.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579182621 none CNC(=O)C1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CCC1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 1, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 5, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 4, 7, 6, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 46, 50, 26, 17, 17, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 46, 46, 46, 50, 50, 50, 50, 17, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 46, 46, 46, 46, 46, 46] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 145 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579182621 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579182621 Building ZINC001579207704 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579207704 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 643) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/643 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/643' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579207704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579207704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579207704 none CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 23, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 23, 23, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 644) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/644 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/644' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579207704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579207704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579207704 none CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 23, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 23, 23, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579207704 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 Building ZINC001579207704 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579207704 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 643) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/643: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579207704.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579207704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579207704 none CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 23, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 23, 23, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 174 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 644) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/644: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579207704.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579207704.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579207704 none CN(CCNc1ccc(c2nn[nH]n2)cn1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'N.ar', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 3, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 12, 23, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 12, 12, 23, 23, 44, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579207704 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579207704 Building ZINC001579225484 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579225484 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 645) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/645 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/645' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579225484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579225484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001579225484 none CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 22, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 22, 22, 41, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 646) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/646 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/646' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579225484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579225484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001579225484 none CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 22, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 22, 22, 42, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579225484 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 Building ZINC001579225484 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579225484 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 645) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/645: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579225484.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579225484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001579225484 none CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 22, 41, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 22, 22, 41, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 646) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/646: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579225484.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579225484.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 47 natoms 46 natoms 45 natoms 44 names: ZINC001579225484 none CN(CCNc1nccnc1c1nn[nH]n1)C(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.pl3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 8, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 16, 22, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 3, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 22, 22, 42, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579225484 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579225484 Building ZINC001579233763 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579233763 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 647) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/647 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/647' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1) `ZINC001579233763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579233763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579233763 none CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 11, 11, 11, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 32, 32, 32, 32] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 648) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/648 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/648' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1) `ZINC001579233763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579233763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579233763 none CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 11, 11, 11, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579233763 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 Building ZINC001579233763 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579233763 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 647) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1) `ZINC001579233763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579233763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579233763 none CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 32, 11, 11, 11, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 32, 32, 32, 32] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 648) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1) `ZINC001579233763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579233763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579233763 none CN(C)CC1(C(=O)N[C@@H]2[C@H]3CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C[C@H]32)CC1 NO_LONG_NAME dock atom types: ['C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 11, 8, 5, 7, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 33, 11, 11, 11, 4, 4, 4, 4, 4, 4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 4, 4, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 11, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 33, 33, 33, 33] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51, 52]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579233763 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579233763 Building ZINC001579240933 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579240933 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 649) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/649 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/649' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001579240933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579240933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001579240933 none CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 14, 31, 31, 31, 33, 33, 33, 33, 33, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 14, 14, 31, 31, 2, 2, 2, 2, 2] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 650) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/650 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/650' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001579240933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579240933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001579240933 none CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 14, 31, 31, 31, 33, 33, 33, 33, 33, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 14, 14, 31, 31, 2, 2, 2, 2, 2] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579240933 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 Building ZINC001579240933 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579240933 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 649) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1) `ZINC001579240933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579240933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001579240933 none CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 14, 31, 31, 31, 33, 33, 33, 33, 33, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 14, 14, 31, 31, 2, 2, 2, 2, 2] 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]) total number of confs: 84 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 650) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1) `ZINC001579240933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579240933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 39 natoms 38 natoms 37 natoms 36 names: ZINC001579240933 none CN(Cc1cc(c2nn[nH]n2)cs1)C(=O)[C@@]([O-])([SiH3])c1cnn(C)c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.2', 'S.3', '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'] dock atom type numbers: [5, 8, 5, 1, 1, 1, 1, 8, 8, 8, 6, 8, 1, 14, 1, 11, 5, 12, 1, 1, 8, 8, 5, 1, 7, 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, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 14, 31, 31, 31, 33, 33, 33, 33, 33, 31, 31, 1, 2, 1, 1, 1, 2, 2, 2, 2, 2, 5, 5, 5, 14, 14, 31, 31, 2, 2, 2, 2, 2] 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]) total number of confs: 85 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579240933 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579240933 Building ZINC001579259071 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579259071 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 651) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/651 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/651' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)CC1) `ZINC001579259071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579259071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259071 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 13, 13, 23, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 13, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 652) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/652 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/652' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)CC1) `ZINC001579259071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579259071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259071 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 18, 18, 26, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 18, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579259071 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 Building ZINC001579259071 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579259071 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 651) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)CC1) `ZINC001579259071.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579259071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259071 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 9, 9, 9, 9, 9, 9, 13, 13, 23, 50, 50, 50, 50, 50, 50, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 13, 50, 50, 50, 50, 50, 50, 9, 9, 9, 9] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 652) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)CC1) `ZINC001579259071.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579259071.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259071 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 18, 18, 26, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 18, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579259071 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259071 Building ZINC001579259072 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579259072 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 653) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/653 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/653' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)CC1) `ZINC001579259072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579259072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259072 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 17, 17, 25, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 17, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 654) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/654 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/654' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)CC1) `ZINC001579259072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579259072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259072 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 22, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 12, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579259072 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 Building ZINC001579259072 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579259072 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 653) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)CC1) `ZINC001579259072.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579259072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259072 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 12, 12, 12, 12, 12, 12, 17, 17, 25, 50, 50, 50, 50, 50, 50, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 12, 12, 17, 50, 50, 50, 50, 50, 50, 12, 12, 12, 12] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 654) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)CC1) `ZINC001579259072.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579259072.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579259072 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2COCCO2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'O.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 12, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 8, 8, 8, 8, 8, 8, 12, 12, 22, 50, 50, 50, 50, 50, 50, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 12, 50, 50, 50, 50, 50, 50, 8, 8, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 155 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579259072 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579259072 Building ZINC001579261426 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579261426 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 655) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/655 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/655' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)CC1) `ZINC001579261426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579261426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579261426 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 20, 20, 31, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 20, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 656) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/656 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/656' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)CC1) `ZINC001579261426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579261426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579261426 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 19, 19, 29, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 19, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579261426 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 Building ZINC001579261426 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579261426 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 655) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)CC1) `ZINC001579261426.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579261426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579261426 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 10, 10, 10, 10, 10, 10, 20, 20, 31, 50, 50, 50, 50, 50, 50, 10, 10, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 10, 10, 20, 50, 50, 50, 50, 50, 10, 10, 10, 10] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 656) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)CC1) `ZINC001579261426.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579261426.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579261426 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N[C@H]1CC[C@@H](NC(=O)[C@H]2CCC(=O)N2)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', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 7, 5, 5, 1, 11, 8, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 4, 13, 13, 13, 13, 13, 13, 19, 19, 29, 50, 50, 50, 50, 50, 50, 13, 13, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 13, 13, 19, 50, 50, 50, 50, 50, 13, 13, 13, 13] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 35, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579261426 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261426 Building ZINC001579261465 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579261465 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 657) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/657 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/657' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 658) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/658 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/658' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 659) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/659 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/659' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 660) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/660 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/660' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579261465 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 Building ZINC001579261465 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579261465 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 657) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 658) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 659) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 660) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579261465 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 Building ZINC001579261465 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579261465 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 657) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 658) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 659) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 660) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579261465 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 Building ZINC001579261465 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579261465 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 657) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/657: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 658) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/658: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 15, 50, 50, 50, 50, 50, 15, 15, 9, 9, 9, 9, 9, 4, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 50, 50, 50, 50, 50, 50, 15, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 659) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/659: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 660) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/660: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579261465.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579261465.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579261465 none C[C@H](NC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'N.am', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 8, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 6, 6, 6, 6, 7, 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, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 50, 50, 50, 50, 50, 14, 14, 8, 8, 8, 8, 8, 4, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579261465 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579261465 Building ZINC001579264925 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579264925 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 661) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/661 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/661' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579264925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264925 none C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 37, 37, 49, 50, 50, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 49, 49, 50, 50, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 662) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/662 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/662' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579264925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264925 none C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 40, 40, 48, 50, 50, 14, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 48, 48, 50, 50, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579264925 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 Building ZINC001579264925 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579264925 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 661) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264925.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579264925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264925 none C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 37, 37, 49, 50, 50, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 37, 37, 37, 49, 49, 50, 50, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 662) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264925.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579264925.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264925 none C[C@@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 14, 40, 40, 48, 50, 50, 14, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 40, 40, 40, 48, 48, 50, 50, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579264925 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264925 Building ZINC001579264926 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579264926 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 663) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/663 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/663' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579264926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264926 none C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 14, 41, 41, 50, 50, 50, 14, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 50, 50, 50, 50, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 664) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/664 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/664' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579264926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264926 none C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 37, 37, 49, 50, 50, 15, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 37, 49, 49, 50, 50, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579264926 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 Building ZINC001579264926 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579264926 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 663) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264926.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579264926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264926 none C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [41, 14, 41, 41, 50, 50, 50, 14, 14, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 41, 41, 41, 50, 50, 50, 50, 14, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 664) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579264926.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579264926.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579264926 none C[C@H](CC(N)=O)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 37, 37, 49, 50, 50, 15, 15, 8, 8, 8, 8, 8, 3, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 37, 37, 37, 49, 49, 50, 50, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579264926 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579264926 Building ZINC001579265951 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265951 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 665) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/665 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/665' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 666) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/666 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/666' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 667) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/667 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/667' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 668) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/668 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/668' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265951 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 Building ZINC001579265951 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265951 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 665) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 666) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 667) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 668) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265951 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 Building ZINC001579265951 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265951 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 665) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 666) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 667) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 668) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265951 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 Building ZINC001579265951 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265951 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 665) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 666) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 667) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/667: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 12, 41, 41, 41, 12, 12, 6, 6, 6, 6, 6, 3, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 50, 50, 50, 50, 50, 41, 41, 41, 12, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 668) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/668: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265951.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265951.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265951 none COC[C@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265951 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265951 Building ZINC001579265954 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265954 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 669) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/669 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/669' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 670) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/670 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/670' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 671) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/671 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/671' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 11, 41, 41, 41, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 672) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/672 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/672' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265954 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 Building ZINC001579265954 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265954 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 669) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 670) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 671) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 11, 41, 41, 41, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 672) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265954 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 Building ZINC001579265954 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265954 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 669) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 670) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 671) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 11, 41, 41, 41, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 672) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265954 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 Building ZINC001579265954 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579265954 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 669) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 11, 42, 42, 42, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 42, 42, 42, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 670) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 671) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/671: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 11, 41, 41, 41, 11, 11, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 11, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 672) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/672: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1) `ZINC001579265954.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579265954.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579265954 none COC[C@@H](OC)C(=O)N[C@H]1CC[C@@H](NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'H', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 7, 12, 5, 1, 11, 8, 5, 7, 5, 5, 5, 7, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 41, 13, 41, 41, 41, 13, 13, 7, 7, 7, 7, 7, 3, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 50, 50, 50, 50, 50, 41, 41, 41, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51, 52, 53]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579265954 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579265954 Building ZINC001579296819 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579296819 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 673) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/673 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/673' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2) `ZINC001579296819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579296819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296819 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 11, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 674) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/674 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/674' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2) `ZINC001579296819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579296819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296819 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [9, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 11, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579296819 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 Building ZINC001579296819 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579296819 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 673) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2) `ZINC001579296819.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579296819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296819 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 11, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 7, 7, 7, 7, 7, 7, 7, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 58 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 674) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2) `ZINC001579296819.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579296819.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296819 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [9, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 11, 21, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 9, 9, 9, 8, 8, 8, 8, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23, 23] 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]) total number of confs: 65 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579296819 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296819 Building ZINC001579296820 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579296820 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 675) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/675 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/675' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2) `ZINC001579296820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579296820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296820 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 15, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 676) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/676 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/676' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2) `ZINC001579296820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579296820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296820 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 15, 20, 23, 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, 23, 23, 23, 23] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579296820 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 Building ZINC001579296820 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579296820 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 675) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2) `ZINC001579296820.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579296820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296820 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [7, 7, 7, 7, 3, 7, 7, 1, 1, 1, 1, 15, 19, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22, 22] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 62 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 676) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2) `ZINC001579296820.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579296820.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579296820 none COc1ccccc1[C@]([O-])([SiH3])C(=O)N1CCc2nc[nH]c2[C@@]12CCNC2 NO_LONG_NAME dock atom types: ['C.3', 'O.3', '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.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 1, 1, 5, 12, 1, 11, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 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, 4, 7, 7, 7, 7, 7, 7, 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: [8, 8, 8, 8, 2, 8, 8, 1, 1, 1, 1, 15, 20, 23, 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, 23, 23, 23, 23] 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]) total number of confs: 67 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579296820 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579296820 Building ZINC001579379103 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379103 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 677) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/677 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/677' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379103 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 678) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/678 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/678' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379103 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379103 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 Building ZINC001579379103 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379103 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 677) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/677: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379103.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379103 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 38, 38, 38, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 172 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 678) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/678: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379103.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379103.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379103 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [24, 12, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379103 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379103 Building ZINC001579379106 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379106 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 679) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/679 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/679' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379106 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 680) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/680 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/680' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379106 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379106 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 Building ZINC001579379106 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379106 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 679) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379106.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379106 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 680) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C) `ZINC001579379106.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379106.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379106 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc2c1nnn2C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 8, 8, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379106 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379106 Building ZINC001579379305 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379305 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 681) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/681 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/681' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379305 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 682) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/682 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/682' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379305 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379305 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 Building ZINC001579379305 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379305 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 681) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379305.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379305 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 157 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 682) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379305.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379305.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379305 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 34, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379305 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379305 Building ZINC001579379307 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379307 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 683) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/683 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/683' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379307 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 684) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/684 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/684' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379307 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379307 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 Building ZINC001579379307 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379307 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 683) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379307.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379307 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 159 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 684) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1) `ZINC001579379307.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379307.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001579379307 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ncn(C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'N.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 8, 1, 8, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 13, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 32, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379307 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379307 Building ZINC001579379492 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379492 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 685) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/685 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/685' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379492 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 18, 18, 18, 38, 50, 50, 18, 18, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 18, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 686) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/686 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/686' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379492 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 20, 20, 20, 38, 50, 50, 20, 20, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 20, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379492 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 Building ZINC001579379492 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379492 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 685) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379492.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379492 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 18, 18, 18, 38, 50, 50, 18, 18, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 18, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 686) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379492.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379492.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379492 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 20, 20, 20, 38, 50, 50, 20, 20, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 20, 38, 38, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 221 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379492 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379492 Building ZINC001579379493 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379493 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 687) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/687 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/687' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379493 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 20, 20, 20, 36, 50, 50, 20, 20, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 20, 36, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 688) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/688 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/688' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379493 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 19, 19, 19, 37, 50, 50, 19, 19, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 19, 37, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379493 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 Building ZINC001579379493 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379493 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 687) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379493.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379493 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 7, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 17, 17, 17, 20, 20, 20, 36, 50, 50, 20, 20, 12, 12, 12, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 20, 36, 36, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 688) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1) `ZINC001579379493.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379493.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379493 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(CC2CC2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 13, 13, 13, 19, 19, 19, 37, 50, 50, 19, 19, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 19, 37, 37, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379493 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379493 Building ZINC001579379712 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379712 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 689) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/689 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/689' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001579379712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379712 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 690) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/690 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/690' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001579379712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379712 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379712 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 Building ZINC001579379712 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379712 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 689) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001579379712.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379712 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 12, 33, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 45, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 191 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 690) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2) `ZINC001579379712.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379712.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379712 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1c2c(nn1C)CCC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 13, 31, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 188 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379712 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379712 Building ZINC001579379762 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379762 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 691) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/691 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/691' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001579379762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379762 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 19, 26, 41, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 26, 26, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 692) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/692 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/692' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001579379762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379762 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 32, 42, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379762 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 Building ZINC001579379762 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379762 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 691) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001579379762.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379762 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 19, 19, 19, 26, 41, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 26, 26, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 186 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 692) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C) `ZINC001579379762.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379762.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379762 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COCc1nccn1C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.2', 'N.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', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 1, 8, 1, 1, 8, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 9, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 23, 23, 23, 32, 42, 50, 50, 50, 50, 50, 50, 17, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 32, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 205 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379762 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379762 Building ZINC001579379796 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379796 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 693) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/693 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/693' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379796 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 694) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/694 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/694' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379796 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379796 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 Building ZINC001579379796 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379796 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 693) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379796.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379796 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 144 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 694) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379796.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379796.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379796 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379796 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379796 Building ZINC001579379797 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379797 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 695) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/695 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/695' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379797 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 696) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/696 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/696' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379797 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379797 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 Building ZINC001579379797 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579379797 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 695) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379797.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579379797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379797 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 33, 33, 33, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 33, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 163 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 696) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1) `ZINC001579379797.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579379797.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579379797 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnc(N(C)C)c1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 8, 5, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 29, 29, 29, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 147 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579379797 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579379797 Building ZINC001579380340 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380340 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 697) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/697 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/697' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380340 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 698) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/698 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/698' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380340 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 49, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380340 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 Building ZINC001579380340 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380340 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 697) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380340 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 23, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 698) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380340 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 49, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380340 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380340 Building ZINC001579380341 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380341 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 699) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/699 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/699' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380341 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 700) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/700 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/700' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380341 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380341 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 Building ZINC001579380341 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380341 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 699) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380341.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380341 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [26, 12, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 700) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2) `ZINC001579380341.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380341.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380341 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc2c([nH]1)CCOC2 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.pl3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 6, 5, 5, 12, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 4, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 24, 24, 24, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 177 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380341 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380341 Building ZINC001579380506 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380506 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 701) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/701 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/701' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380506 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 702) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/702 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/702' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380506 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380506 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 Building ZINC001579380506 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380506 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 701) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380506.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380506 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 702) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380506.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380506.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380506 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380506 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380506 Building ZINC001579380507 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380507 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 703) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/703 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/703' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380507 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 704) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/704 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/704' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380507 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380507 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 Building ZINC001579380507 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380507 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 703) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380507.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380507 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 35, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 704) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21) `ZINC001579380507.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380507.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380507 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cncc2ncn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'N.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', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 8, 1, 8, 5, 1, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 12, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 37, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 163 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380507 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380507 Building ZINC001579380656 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380656 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 705) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/705 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/705' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F) `ZINC001579380656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380656 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 27, 27, 27, 27, 27, 50, 50, 50, 10, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 27, 27, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 706) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/706 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/706' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F) `ZINC001579380656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380656 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 27, 27, 27, 27, 27, 50, 50, 50, 8, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 27, 27, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380656 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 Building ZINC001579380656 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579380656 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 705) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F) `ZINC001579380656.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579380656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380656 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 15, 15, 15, 27, 27, 27, 27, 27, 50, 50, 50, 10, 10, 10, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 27, 27, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 706) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F) `ZINC001579380656.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579380656.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579380656 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1ccnn1CC(F)F NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.3', 'F', '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, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 15, 15, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 13, 13, 13, 27, 27, 27, 27, 27, 50, 50, 50, 8, 8, 8, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 27, 27, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579380656 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579380656 Building ZINC001579383612 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383612 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 707) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/707 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/707' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 708) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/708 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/708' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 709) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/709 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/709' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 710) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/710 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/710' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383612 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 Building ZINC001579383612 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383612 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 707) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 708) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 709) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 710) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383612 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 Building ZINC001579383612 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383612 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 707) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 708) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 709) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 710) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383612 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 Building ZINC001579383612 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383612 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 707) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 708) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 709) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/709: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 15, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 710) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/710: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383612.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383612.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383612 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 18, 18, 18, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383612 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383612 Building ZINC001579383613 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383613 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 711) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/711 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/711' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 16, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 712) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/712 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/712' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 713) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/713 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/713' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 714) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/714 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/714' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383613 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 Building ZINC001579383613 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383613 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 711) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 16, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 712) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 713) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 714) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383613 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 Building ZINC001579383613 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383613 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 711) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 16, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 712) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 713) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 714) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383613 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 Building ZINC001579383613 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001579383613 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 711) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 16, 22, 22, 27, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 16, 16, 16, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 712) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 713) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/713: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [17, 10, 17, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 22, 22, 26, 48, 48, 48, 48, 48, 48, 50, 50, 48, 48, 17, 17, 17, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 48, 48, 48, 48, 50, 50, 48, 48, 48, 48] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 714) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/714: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1) `ZINC001579383613.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001579383613.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 7 0 4 7 1 4 7 2 3 7 2 10 to be deleted 11 to be deleted 12 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579383613 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[C@@H](C(N)=O)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'N.am', 'O.2', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 7, 1, 8, 11, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [11, 6, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 15, 15, 16, 43, 43, 43, 43, 43, 43, 50, 50, 43, 43, 11, 11, 11, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 43, 43, 43, 43, 50, 50, 43, 43, 43, 43] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383613 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383613 Building ZINC001579383912 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579383912 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 715) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/715 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/715' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579383912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579383912 none Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 24, 17, 4, 4, 4, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 27, 27, 27, 27, 17, 17, 4, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 716) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/716 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/716' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579383912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579383912 none Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 25, 21, 7, 7, 7, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 30, 29, 30, 30, 21, 21, 7, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383912 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 Building ZINC001579383912 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579383912 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 715) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579383912.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579383912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579383912 none Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 27, 24, 17, 4, 4, 4, 3, 2, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 27, 27, 27, 27, 17, 17, 4, 3, 3, 3, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 49, 40, 41, 42, 43, 44, 45, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 46, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 716) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001579383912.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579383912.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579383912 none Cc1noc(CCCC(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'O.3', 'C.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 12, 1, 5, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 3, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 30, 25, 21, 7, 7, 7, 5, 5, 5, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 30, 29, 30, 30, 21, 21, 7, 5, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579383912 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579383912 Building ZINC001579384049 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384049 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 717) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/717 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/717' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O) `ZINC001579384049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384049 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 43, 43, 43, 47, 47, 46, 47, 50, 50, 47, 47, 47, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 47, 50, 50, 50, 50, 50, 94] 100 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 287 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 718) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/718 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/718' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O) `ZINC001579384049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384049 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 49, 49, 35, 49, 50, 50, 49, 49, 49, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 49, 50, 50, 50, 50, 50, 98] 100 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 305 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384049 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 Building ZINC001579384049 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384049 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 717) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O) `ZINC001579384049.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384049 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 30, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 43, 43, 43, 47, 47, 46, 47, 50, 50, 47, 47, 47, 30, 30, 30, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 43, 47, 50, 50, 50, 50, 50, 94] 100 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 287 number of broken/clashed sets: 31 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 718) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O) `ZINC001579384049.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384049.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384049 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnc(C2CC2)nc1O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 1, 5, 5, 5, 8, 1, 12, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 7, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [21, 10, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 35, 35, 35, 49, 49, 35, 49, 50, 50, 49, 49, 49, 21, 21, 21, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 49, 50, 50, 50, 50, 50, 98] 100 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 305 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384049 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384049 Building ZINC001579384060 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384060 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 719) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/719 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/719' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384060 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 720) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/720 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/720' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384060 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 21, 21, 21, 44, 45, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 44, 44, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384060 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 Building ZINC001579384060 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384060 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 719) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384060.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384060 none C[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 26, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 216 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 720) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384060.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384060.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384060 none C[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 21, 21, 21, 44, 45, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 44, 44, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384060 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384060 Building ZINC001579384061 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384061 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 721) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/721 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/721' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384061 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 20, 20, 20, 44, 45, 50, 50, 50, 50, 50, 50, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 44, 44, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 722) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/722 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/722' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384061 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384061 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 Building ZINC001579384061 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384061 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 721) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384061.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384061 none C[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [14, 7, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 20, 20, 20, 44, 45, 50, 50, 50, 50, 50, 50, 14, 14, 14, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 20, 44, 44, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 722) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O) `ZINC001579384061.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384061.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001579384061 none C[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CCn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [22, 10, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 22, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 27, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 39, 37, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 40, 41, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384061 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384061 Building ZINC001579384109 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384109 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 723) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/723 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/723' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384109 none COCC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 29, 29, 29, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 29, 21, 21, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 724) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/724 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/724' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384109 none COCC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 25, 25, 25, 22, 13, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 25, 22, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384109 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 Building ZINC001579384109 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384109 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 723) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384109.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384109 none COCC1(C(=O)N[C@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 35, 29, 29, 29, 21, 11, 21, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 50, 50, 50, 50, 50, 29, 21, 21, 21, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 724) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384109.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384109.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384109 none COCC1(C(=O)N[C@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 25, 25, 25, 22, 13, 22, 22, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 50, 50, 50, 50, 50, 25, 22, 22, 22, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 32, 32, 32, 32, 32, 32, 32] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 213 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384109 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384109 Building ZINC001579384110 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384110 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 725) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/725 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/725' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384110 none COCC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 22, 22, 22, 20, 11, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 22, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 726) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/726 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/726' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COCC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384110 none COCC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 29, 28, 28, 20, 11, 20, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 28, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384110 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 Building ZINC001579384110 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579384110 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 725) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384110.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579384110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384110 none COCC1(C(=O)N[C@@H](C)CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 29, 22, 22, 22, 20, 11, 20, 20, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 50, 50, 50, 50, 50, 22, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29, 29, 29, 29, 29, 29, 29] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 218 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 726) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COCC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1) `ZINC001579384110.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579384110.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 14 is the cov attach 4 14 0 4 14 1 4 14 2 3 14 2 17 to be deleted 18 to be deleted 19 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001579384110 none COCC1(C(=O)N[C@@H](C)CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 5, 5, 1, 11, 8, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 6, 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, 6, 4, 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, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 34, 29, 28, 28, 20, 11, 20, 19, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 50, 50, 50, 50, 50, 28, 20, 20, 20, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 34, 34, 34, 34, 34, 34, 34, 34] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 12, 45, 14, 15, 16, 17, 18, 19, 44] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 215 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579384110 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579384110 Building ZINC001579622275 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579622275 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 727) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/727 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/727' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579622275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579622275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622275 none Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 28, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 44, 28, 28, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 728) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/728 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/728' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579622275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579622275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622275 none Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 28, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 28, 28, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579622275 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 Building ZINC001579622275 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579622275 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 727) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579622275.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579622275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622275 none Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 44, 44, 44, 28, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 44, 28, 28, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 182 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 728) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579622275.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579622275.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622275 none Cc1nn2cccnc2c1C(=O)NC[C@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 43, 43, 43, 28, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 43, 28, 28, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 176 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579622275 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622275 Building ZINC001579622276 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579622276 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 729) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/729 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/729' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579622276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579622276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622276 none Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 26, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 26, 26, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 730) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/730 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/730' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579622276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579622276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622276 none Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 27, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 27, 27, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579622276 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 Building ZINC001579622276 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579622276 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 729) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579622276.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579622276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622276 none Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 41, 41, 41, 26, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 41, 26, 26, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 730) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579622276.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579622276.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579622276 none Cc1nn2cccnc2c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 42, 42, 42, 27, 8, 2, 8, 8, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 42, 27, 27, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 179 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579622276 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579622276 Building ZINC001579649203 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579649203 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 731) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/731 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/731' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579649203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579649203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579649203 none C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens 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, 9, 9, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 732) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/732 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/732' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579649203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579649203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579649203 none C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579649203 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 Building ZINC001579649203 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579649203 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 731) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579649203.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579649203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579649203 none C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens 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, 9, 9, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 732) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579649203.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579649203.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579649203 none C[C@H](CNC(=O)c1cnc(N(C)C)cn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'C.3', 'C.3', 'C.ar', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 5, 5, 1, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 3, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 26, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 178 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579649203 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579649203 Building ZINC001579722696 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579722696 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 733) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/733 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/733' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579722696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579722696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579722696 none C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 11, 11, 11, 21, 18, 27, 30, 30, 30, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 21, 21, 21, 25, 25, 30, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 734) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/734 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/734' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579722696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579722696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579722696 none C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 16, 12, 24, 28, 28, 28, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 16, 16, 16, 16, 20, 21, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579722696 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 Building ZINC001579722696 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579722696 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 733) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579722696.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579722696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579722696 none C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 11, 11, 11, 11, 21, 18, 27, 30, 30, 30, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 11, 11, 11, 21, 21, 21, 21, 25, 25, 30, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 229 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 734) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579722696.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579722696.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579722696 none C[C@@H](CNC(=O)CCCNC(=O)C1CC1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 5, 5, 8, 1, 11, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 8, 8, 8, 16, 12, 24, 28, 28, 28, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3, 3, 6, 6, 8, 16, 16, 16, 16, 20, 21, 28, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 222 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579722696 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579722696 Building ZINC001579733197 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579733197 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 735) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/735 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/735' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579733197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579733197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733197 none C[C@@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 8, 8, 8, 28, 42, 42, 42, 50, 50, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 28, 28, 42, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 736) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/736 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/736' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579733197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579733197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733197 none C[C@@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 13, 13, 13, 32, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 13, 32, 32, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579733197 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 Building ZINC001579733197 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579733197 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 735) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579733197.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579733197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733197 none C[C@@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 8, 8, 8, 28, 42, 42, 42, 50, 50, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 28, 28, 42, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 166 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 736) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579733197.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579733197.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733197 none C[C@@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 13, 13, 13, 32, 40, 40, 40, 50, 50, 40, 40, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 13, 32, 32, 40, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579733197 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733197 Building ZINC001579733198 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579733198 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 737) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/737 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/737' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579733198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579733198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733198 none C[C@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 14, 14, 14, 32, 42, 42, 42, 50, 50, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 32, 32, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 738) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/738 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/738' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579733198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579733198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733198 none C[C@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 8, 8, 8, 27, 43, 43, 43, 50, 50, 43, 43, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 27, 27, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579733198 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 Building ZINC001579733198 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579733198 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 737) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579733198.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579733198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733198 none C[C@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 5, 14, 14, 14, 32, 42, 42, 42, 50, 50, 42, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 5, 5, 14, 32, 32, 42, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 48, 39, 40, 41, 42, 43, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 738) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579733198.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579733198.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579733198 none C[C@H](CNC(=O)Cn1cc(C2CC2)nn1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 5, 5, 5, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 4, 8, 8, 8, 27, 43, 43, 43, 50, 50, 43, 43, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 27, 27, 43, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 160 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579733198 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579733198 Building ZINC001579739226 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579739226 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 739) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/739 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/739' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579739226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579739226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739226 none C[C@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 18, 36, 36, 36, 42, 42, 42, 42, 42, 42, 50, 50, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 36, 42, 84, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 740) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/740 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/740' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579739226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579739226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739226 none C[C@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens 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, 2, 6, 6, 16, 38, 38, 38, 42, 42, 42, 42, 42, 42, 50, 50, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 38, 42, 84, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579739226 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 Building ZINC001579739226 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579739226 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 739) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579739226.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579739226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739226 none C[C@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 18, 36, 36, 36, 42, 42, 42, 42, 42, 42, 50, 50, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 36, 42, 84, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 254 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 740) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579739226.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579739226.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739226 none C[C@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens 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, 2, 6, 6, 16, 38, 38, 38, 42, 42, 42, 42, 42, 42, 50, 50, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 16, 16, 38, 42, 84, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 257 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579739226 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739226 Building ZINC001579739227 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579739227 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 741) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/741 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/741' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579739227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579739227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739227 none C[C@@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 13, 33, 33, 33, 38, 38, 38, 38, 38, 38, 50, 50, 38, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 33, 38, 76, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 742) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/742 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/742' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579739227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579739227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739227 none C[C@@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 18, 34, 34, 34, 41, 41, 41, 41, 41, 41, 50, 50, 41, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 34, 41, 82, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579739227 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 Building ZINC001579739227 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579739227 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 741) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579739227.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579739227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739227 none C[C@@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 13, 33, 33, 33, 38, 38, 38, 38, 38, 38, 50, 50, 38, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 33, 38, 76, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 252 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 742) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579739227.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579739227.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001579739227 none C[C@@H](CNC(=O)c1cc(O)nc(C2CC2)n1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'C.ar', 'C.3', 'C.3', 'C.3', 'N.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 1, 12, 8, 1, 5, 5, 5, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 4, 3, 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] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [5, 2, 5, 5, 18, 34, 34, 34, 41, 41, 41, 41, 41, 41, 50, 50, 41, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 18, 18, 34, 41, 82, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 100 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 250 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579739227 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579739227 Building ZINC001579747325 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579747325 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 743) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/743 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/743' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579747325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579747325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579747325 none C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 30, 30, 30, 41, 43, 43, 41, 41, 50, 50, 43, 43, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 30, 41, 41, 43, 43, 50, 50, 43, 43, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 744) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/744 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/744' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579747325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579747325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579747325 none C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 11, 26, 26, 26, 41, 42, 42, 41, 41, 50, 50, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 26, 41, 41, 42, 42, 50, 50, 42, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579747325 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 Building ZINC001579747325 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579747325 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 743) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/743: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579747325.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579747325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579747325 none C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 30, 30, 30, 41, 43, 43, 41, 41, 50, 50, 43, 43, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 30, 41, 41, 43, 43, 50, 50, 43, 43, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 211 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 744) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/744: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579747325.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579747325.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579747325 none C[C@@H](CNC(=O)Cc1ccc(C(N)=O)cc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 1, 1, 1, 1, 1, 8, 11, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 6, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 11, 26, 26, 26, 41, 42, 42, 41, 41, 50, 50, 42, 42, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 11, 11, 26, 41, 41, 42, 42, 50, 50, 42, 42, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579747325 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579747325 Building ZINC001579783503 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579783503 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 745) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/745 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/745' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579783503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579783503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579783503 none C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 15, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 27, 50, 150, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 746) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/746 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/746' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579783503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579783503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579783503 none C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 17, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 28, 50, 150, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579783503 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 Building ZINC001579783503 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579783503 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 745) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/745: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579783503.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579783503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579783503 none C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [6, 2, 6, 6, 15, 27, 27, 27, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 15, 15, 27, 50, 150, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 295 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 746) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/746: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579783503.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579783503.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 49 natoms 48 natoms 47 natoms 46 names: ZINC001579783503 none C[C@@H](CNC(=O)c1cnc2[nH]c(O)nc2c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'C.2', 'O.3', 'N.2', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 1, 8, 6, 1, 12, 8, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 3, 7, 4, 7, 7, 4, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 5, 5, 17, 28, 28, 28, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 17, 17, 28, 50, 150, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 150 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 19, 21, 22, 23, 24, 25, 26] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 20, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 287 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579783503 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579783503 Building ZINC001579846856 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579846856 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 747) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/747 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/747' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579846856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579846856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846856 none C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 30, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 748) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/748 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/748' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579846856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579846856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846856 none C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579846856 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 Building ZINC001579846856 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579846856 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 747) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/747: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579846856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579846856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846856 none C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 30, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 183 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 748) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/748: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579846856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579846856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846856 none C[C@@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579846856 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846856 Building ZINC001579846858 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579846858 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 749) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/749 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/749' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579846858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579846858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846858 none C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 750) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/750 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/750' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579846858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579846858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846858 none C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 30, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579846858 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 Building ZINC001579846858 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579846858 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 749) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579846858.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579846858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846858 none C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 29, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 29, 29, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 750) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579846858.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579846858.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001579846858 none C[C@H](CNC(=O)c1cnn2cccnc12)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 2, 10, 10, 30, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 10, 10, 30, 30, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [36, 37, 38, 39, 40, 41, 42, 43, 44, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35]) total number of confs: 185 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579846858 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579846858 Building ZINC001579857905 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579857905 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 751) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/751 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/751' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579857905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579857905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579857905 none C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 16, 16, 16, 33, 27, 41, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 16, 33, 33, 37, 37, 39, 41, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 266 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 752) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/752 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/752' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579857905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579857905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579857905 none C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 12, 12, 12, 36, 23, 40, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 12, 36, 36, 37, 37, 37, 40, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579857905 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 Building ZINC001579857905 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579857905 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 751) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/751: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579857905.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579857905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579857905 none C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 14, 16, 16, 16, 33, 27, 41, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 14, 14, 16, 33, 33, 37, 37, 39, 41, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 266 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 752) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/752: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579857905.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579857905.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001579857905 none C[C@@H](CNC(=O)CCCn1ccccc1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 5, 5, 8, 1, 1, 1, 1, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 10, 12, 12, 12, 36, 23, 40, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 10, 10, 12, 36, 36, 37, 37, 37, 40, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 43, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 281 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579857905 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579857905 Building ZINC001579870391 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579870391 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 753) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/753 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/753' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579870391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579870391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001579870391 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 45, 45, 24, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 24, 24, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 754) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/754 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/754' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579870391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579870391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001579870391 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 47, 47, 26, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 26, 26, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579870391 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 Building ZINC001579870391 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579870391 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 753) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579870391.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579870391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001579870391 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 45, 45, 45, 24, 9, 2, 9, 9, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 45, 24, 24, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 174 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 754) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579870391.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579870391.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001579870391 none Cc1nn(C)c(F)c1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'F', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 15, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 47, 47, 26, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 47, 26, 26, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579870391 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579870391 Building ZINC001579886449 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579886449 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 755) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/755 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/755' -> `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]1CNC[C@@H]1O) `ZINC001579886449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579886449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001579886449 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CNC[C@@H]1O 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', 'N.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 11, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 6, 31, 31, 31, 31, 31, 93] 150 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]) total number of confs: 199 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 756) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/756 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/756' -> `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]1CNC[C@@H]1O) `ZINC001579886449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579886449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001579886449 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CNC[C@@H]1O 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', 'N.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 12, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 6, 34, 34, 34, 34, 34, 102] 150 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579886449 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 Building ZINC001579886449 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579886449 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 755) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CNC[C@@H]1O) `ZINC001579886449.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579886449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001579886449 none Cc1nn(c2ccccc2)c(C)c1[C@@]([O-])([SiH3])C(=O)N[C@@H]1CNC[C@@H]1O 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', 'N.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 11, 31, 31, 31, 31, 31, 31, 31, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 6, 31, 31, 31, 31, 31, 93] 150 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]) total number of confs: 199 number of broken/clashed sets: 22 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 756) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CNC[C@@H]1O) `ZINC001579886449.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579886449.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 13 is the cov attach 4 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: ZINC001579886449 none Cc1nn(c2ccccc2)c(C)c1[C@]([O-])([SiH3])C(=O)N[C@@H]1CNC[C@@H]1O 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', 'N.3', 'C.3', 'C.3', 'H', '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, 8, 1, 1, 1, 1, 1, 1, 1, 5, 1, 5, 12, 1, 11, 8, 5, 7, 5, 10, 5, 5, 7, 12, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 6] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 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] 1 hydrogens 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, 4, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 1, 1, 1, 1, 6, 6, 12, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 12, 12, 7, 12, 12, 4, 4, 4, 6, 34, 34, 34, 34, 34, 102] 150 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]) total number of confs: 216 number of broken/clashed sets: 27 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579886449 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579886449 Building ZINC001579889259 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889259 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 757) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/757 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/757' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 758) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/758 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/758' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889259 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 Building ZINC001579889259 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889259 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 757) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889259.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889259 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 9, 21, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 57 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 758) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889259.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889259.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889259 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 8, 18, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 59 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889259 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889259 Building ZINC001579889260 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889260 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 759) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/759 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/759' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889260 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 760) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/760 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/760' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889260 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889260 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 Building ZINC001579889260 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889260 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 759) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889260.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889260 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 17, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 760) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889260.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889260.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889260 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 49 conformations in input total number of sets (complete confs): 49 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 12, 16, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 37, 37, 37, 37, 37, 37, 37, 37] 49 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889260 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889260 Building ZINC001579889261 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889261 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 761) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/761 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/761' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889261 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 762) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/762 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/762' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889261 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889261 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 Building ZINC001579889261 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889261 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 761) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889261.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889261 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 22, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 68 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 762) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1) `ZINC001579889261.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889261.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889261 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@H](C(F)(F)F)[C@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 19, 22, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 36, 4, 4, 4, 4, 4, 4, 4, 4, 4, 36, 36, 36, 36, 36, 36, 36, 36] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 69 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889261 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889261 Building ZINC001579889262 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889262 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 763) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/763 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/763' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889262 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 764) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/764 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/764' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889262 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889262 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 Building ZINC001579889262 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889262 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 763) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889262.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889262 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 21, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 37, 4, 4, 4, 4, 4, 4, 4, 4, 4, 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]) total number of confs: 68 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 764) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1) `ZINC001579889262.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889262.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001579889262 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CC[C@@H](C(F)(F)F)[C@@H](N)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'F', 'F', 'F', 'C.3', 'H', 'N.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 15, 15, 15, 5, 7, 10, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 14, 19, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 4, 4, 4, 4, 4, 4, 4, 4, 4, 35, 35, 35, 35, 35, 35, 35, 35] 50 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 65 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889262 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889262 Building ZINC001579889686 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889686 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 765) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/765 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/765' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1) `ZINC001579889686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889686 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 12, 12, 12, 12, 12, 23, 40, 40, 40, 40, 40, 40, 40, 40, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 12, 12] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 766) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/766 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/766' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1) `ZINC001579889686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889686 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 6, 11, 11, 11, 11, 11, 24, 39, 39, 39, 39, 39, 39, 39, 39, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889686 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 Building ZINC001579889686 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889686 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 765) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1) `ZINC001579889686.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889686 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 12, 12, 12, 12, 12, 23, 40, 40, 40, 40, 40, 40, 40, 40, 12, 3, 3, 3, 3, 3, 3, 3, 3, 3, 12, 12, 12, 12, 12, 12, 40, 40, 40, 40, 40, 40, 40, 40, 12, 12] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 98 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 766) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1) `ZINC001579889686.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889686.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889686 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 6, 11, 11, 11, 11, 11, 24, 39, 39, 39, 39, 39, 39, 39, 39, 11, 4, 4, 4, 4, 4, 4, 4, 4, 4, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889686 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889686 Building ZINC001579889687 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889687 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 767) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/767 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/767' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1) `ZINC001579889687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889687 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 8, 11, 11, 11, 11, 11, 22, 39, 39, 39, 39, 39, 39, 39, 39, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 768) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/768 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/768' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1) `ZINC001579889687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889687 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 5, 9, 9, 9, 9, 9, 22, 37, 37, 37, 37, 37, 37, 37, 37, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889687 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 Building ZINC001579889687 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889687 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 767) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1) `ZINC001579889687.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889687 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 8, 11, 11, 11, 11, 11, 22, 39, 39, 39, 39, 39, 39, 39, 39, 11, 3, 3, 3, 3, 3, 3, 3, 3, 3, 11, 11, 11, 11, 11, 11, 39, 39, 39, 39, 39, 39, 39, 39, 11, 11] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 95 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 768) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1) `ZINC001579889687.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889687.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889687 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 3, 5, 9, 9, 9, 9, 9, 22, 37, 37, 37, 37, 37, 37, 37, 37, 9, 4, 4, 4, 4, 4, 4, 4, 4, 4, 9, 9, 9, 9, 9, 9, 37, 37, 37, 37, 37, 37, 37, 37, 9, 9] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 90 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889687 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889687 Building ZINC001579889688 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889688 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 769) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/769 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/769' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1) `ZINC001579889688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889688 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 13, 13, 13, 13, 13, 15, 35, 35, 35, 35, 35, 35, 35, 35, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 770) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/770 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/770' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1) `ZINC001579889688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889688 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 7, 13, 13, 13, 13, 13, 19, 40, 40, 40, 40, 40, 40, 40, 40, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 13, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889688 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 Building ZINC001579889688 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889688 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 769) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/769: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1) `ZINC001579889688.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889688 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 5, 9, 13, 13, 13, 13, 13, 15, 35, 35, 35, 35, 35, 35, 35, 35, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 35, 35, 35, 35, 35, 35, 35, 35, 13, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 92 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 770) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/770: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1) `ZINC001579889688.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889688.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889688 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@H]2C[C@@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 7, 13, 13, 13, 13, 13, 19, 40, 40, 40, 40, 40, 40, 40, 40, 13, 3, 3, 3, 3, 3, 3, 3, 3, 3, 13, 13, 13, 13, 13, 13, 40, 40, 40, 40, 40, 40, 40, 40, 13, 13] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 97 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889688 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889688 Building ZINC001579889689 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889689 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 771) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/771 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/771' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1) `ZINC001579889689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889689 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 16, 16, 16, 16, 16, 22, 40, 40, 40, 40, 40, 40, 40, 40, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 772) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/772 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/772' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1) `ZINC001579889689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889689 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 9, 14, 14, 14, 14, 14, 23, 41, 41, 41, 41, 41, 41, 41, 41, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889689 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 Building ZINC001579889689 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579889689 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 771) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/771: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1) `ZINC001579889689.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579889689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889689 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 3, 3, 3, 3, 3, 3, 1, 1, 1, 2, 4, 8, 16, 16, 16, 16, 16, 22, 40, 40, 40, 40, 40, 40, 40, 40, 16, 3, 3, 3, 3, 3, 3, 3, 3, 3, 16, 16, 16, 16, 16, 16, 40, 40, 40, 40, 40, 40, 40, 40, 16, 16] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 99 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 772) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/772: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1) `ZINC001579889689.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579889689.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579889689 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)N1CCC[C@H]([C@@H]2C[C@H](N)CCO2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'C.2', 'C.3', 'C.2', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'H', 'C.3', 'C.3', 'H', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 5, 1, 5, 1, 5, 12, 1, 11, 8, 5, 5, 5, 5, 7, 5, 7, 5, 5, 7, 10, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 4, 4, 4, 4, 4, 4, 1, 1, 1, 2, 6, 9, 14, 14, 14, 14, 14, 23, 41, 41, 41, 41, 41, 41, 41, 41, 14, 4, 4, 4, 4, 4, 4, 4, 4, 4, 14, 14, 14, 14, 14, 14, 41, 41, 41, 41, 41, 41, 41, 41, 14, 14] 50 rigid atoms, others: [8, 9, 7] set([0, 1, 2, 3, 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 107 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579889689 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579889689 Building ZINC001579936432 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579936432 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 773) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/773 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/773' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579936432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579936432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579936432 none Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 33, 17, 17, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 774) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/774 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/774' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579936432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579936432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579936432 none Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 31, 18, 18, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579936432 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 Building ZINC001579936432 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579936432 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 773) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579936432.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579936432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579936432 none Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 33, 17, 17, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 151 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 774) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579936432.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579936432.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001579936432 none Cc1nc2ccnn2cc1C(=O)NC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 1, 1, 11, 8, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 18, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 31, 18, 18, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 159 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579936432 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579936432 Building ZINC001579959497 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579959497 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 775) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/775 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/775' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579959497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579959497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959497 none C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 28, 28, 28, 44, 49, 50, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 28, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 776) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/776 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/776' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579959497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579959497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959497 none C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 16, 32, 32, 32, 48, 47, 50, 47, 50, 50, 47, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 32, 48, 48, 50, 50, 50, 47, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 243 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579959497 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 Building ZINC001579959497 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579959497 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 775) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579959497.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579959497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959497 none C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 12, 28, 28, 28, 44, 49, 50, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 12, 12, 28, 44, 44, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 210 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 776) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579959497.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579959497.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959497 none C[C@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 16, 32, 32, 32, 48, 47, 50, 47, 50, 50, 47, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 32, 48, 48, 50, 50, 50, 47, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 243 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579959497 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959497 Building ZINC001579959498 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579959498 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 777) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/777 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/777' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579959498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579959498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959498 none C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 17, 31, 31, 31, 47, 48, 50, 48, 50, 50, 48, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 31, 47, 47, 50, 50, 50, 48, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 236 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 778) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/778 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/778' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579959498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579959498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959498 none C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 29, 29, 29, 44, 49, 50, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 29, 44, 44, 50, 50, 50, 49, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579959498 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 Building ZINC001579959498 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579959498 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 777) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579959498.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579959498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959498 none C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 17, 31, 31, 31, 47, 48, 50, 48, 50, 50, 48, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 17, 17, 31, 47, 47, 50, 50, 50, 48, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 236 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 778) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579959498.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579959498.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001579959498 none C[C@@H](CNC(=O)CNC(=O)c1ccccc1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [6, 2, 6, 6, 13, 29, 29, 29, 44, 49, 50, 49, 50, 50, 49, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 6, 6, 6, 13, 13, 29, 44, 44, 50, 50, 50, 49, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [41, 42, 43, 44, 45, 46, 47, 48, 49, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 208 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579959498 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579959498 Building ZINC001579990231 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579990231 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 779) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/779 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/779' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579990231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579990231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990231 none C[C@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 780) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/780 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/780' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579990231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579990231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990231 none C[C@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 19, 40, 40, 40, 49, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 40, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579990231 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 Building ZINC001579990231 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579990231 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 779) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579990231.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579990231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990231 none C[C@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 780) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579990231.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579990231.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990231 none C[C@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 19, 40, 40, 40, 49, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 40, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 197 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579990231 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990231 Building ZINC001579990232 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579990232 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 781) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/781 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/781' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579990232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579990232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990232 none C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 19, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 201 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 782) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/782 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/782' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579990232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579990232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990232 none C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579990232 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 Building ZINC001579990232 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001579990232 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 781) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/781: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001579990232.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001579990232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990232 none C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 9, 19, 40, 40, 40, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 9, 9, 19, 19, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 201 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 782) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/782: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001579990232.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001579990232.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001579990232 none C[C@@H](CNC(=O)CN1CCCCCC1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 8, 1, 11, 5, 8, 5, 5, 5, 5, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 36, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 44, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 202 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001579990232 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001579990232 Building ZINC001580019662 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580019662 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 783) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/783 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/783' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580019662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019662 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 43, 43, 43, 43, 43, 45, 45, 50, 50, 50, 50, 50, 50, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 43, 43, 43, 43, 50, 50, 100, 43, 43] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 784) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/784 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/784' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580019662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019662 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 42, 42, 42, 42, 42, 45, 45, 50, 50, 50, 50, 50, 50, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 42, 42, 42, 42, 50, 50, 100, 42, 42] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580019662 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 Building ZINC001580019662 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580019662 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 783) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019662.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580019662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019662 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 15, 43, 43, 43, 43, 43, 45, 45, 50, 50, 50, 50, 50, 50, 43, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 9, 9, 43, 43, 43, 43, 50, 50, 100, 43, 43] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 784) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019662.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580019662.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019662 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 19, 42, 42, 42, 42, 42, 45, 45, 50, 50, 50, 50, 50, 50, 42, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 12, 12, 42, 42, 42, 42, 50, 50, 100, 42, 42] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 240 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580019662 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019662 Building ZINC001580019663 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580019663 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 785) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/785 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/785' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580019663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 44, 44, 44, 44, 44, 44, 44, 50, 50, 50, 50, 50, 50, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 44, 44, 44, 50, 50, 100, 44, 44] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 786) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/786 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/786' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580019663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 41, 41, 41, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 41, 41, 41, 41, 50, 50, 100, 41, 41] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580019663 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 Building ZINC001580019663 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580019663 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 785) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/785: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019663.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580019663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019663 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 21, 44, 44, 44, 44, 44, 44, 44, 50, 50, 50, 50, 50, 50, 44, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 13, 13, 44, 44, 44, 44, 50, 50, 100, 44, 44] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 238 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 786) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/786: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1) `ZINC001580019663.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580019663.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 49 natoms 48 natoms 47 natoms 46 names: ZINC001580019663 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2ccc(O)nn2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'N.ar', 'N.ar', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 12, 8, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 3, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 100 conformations in input total number of sets (complete confs): 100 using faster count positions algorithm for large data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 18, 41, 41, 41, 41, 41, 43, 43, 50, 50, 50, 50, 50, 50, 41, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 10, 10, 41, 41, 41, 41, 50, 50, 100, 41, 41] 100 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 25, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]) total number of confs: 235 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580019663 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580019663 Building ZINC001580046811 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046811 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 787) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/787 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/787' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046811 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 21, 32, 32, 32, 42, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 21, 32, 42, 42, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 788) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/788 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/788' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046811 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 14, 34, 34, 34, 44, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 34, 44, 44, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046811 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 Building ZINC001580046811 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046811 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 787) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046811.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046811 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 4, 7, 8, 8, 8, 8, 8, 21, 32, 32, 32, 42, 50, 50, 50, 50, 50, 50, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 21, 21, 32, 42, 42, 50, 50, 50, 50, 8, 8] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 788) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046811.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046811.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046811 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 14, 34, 34, 34, 44, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 34, 44, 44, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046811 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046811 Building ZINC001580046812 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046812 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 789) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/789 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/789' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046812 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 14, 33, 33, 33, 44, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 33, 44, 44, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 790) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/790 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/790' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046812 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 7, 20, 31, 31, 31, 42, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 31, 42, 42, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046812 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 Building ZINC001580046812 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046812 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 789) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/789: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046812.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046812 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 6, 6, 6, 6, 6, 14, 33, 33, 33, 44, 50, 50, 50, 50, 50, 50, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 14, 14, 33, 44, 44, 50, 50, 50, 50, 6, 6] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 178 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 790) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/790: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1) `ZINC001580046812.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046812.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580046812 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)Cn2ccccc2=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 6, 7, 7, 7, 7, 7, 20, 31, 31, 31, 42, 50, 50, 50, 50, 50, 50, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7, 7, 7, 20, 20, 31, 42, 42, 50, 50, 50, 50, 7, 7] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046812 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046812 Building ZINC001580046825 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046825 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 791) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/791 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/791' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1) `ZINC001580046825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046825 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 25, 39, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 25, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 792) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/792 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/792' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1) `ZINC001580046825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046825 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 21, 35, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 21, 21, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046825 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 Building ZINC001580046825 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046825 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 791) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/791: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1) `ZINC001580046825.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046825 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 13, 13, 13, 25, 39, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 13, 25, 25, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 792) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/792: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1) `ZINC001580046825.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046825.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046825 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 21, 35, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 6, 21, 21, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046825 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046825 Building ZINC001580046826 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046826 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 793) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/793 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/793' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1) `ZINC001580046826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046826 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 20, 34, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 20, 20, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 794) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/794 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/794' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1) `ZINC001580046826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046826 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 26, 40, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 26, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046826 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 Building ZINC001580046826 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046826 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 793) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/793: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1) `ZINC001580046826.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046826 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 7, 7, 7, 20, 34, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 7, 20, 20, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 794) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/794: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1) `ZINC001580046826.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046826.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 50 natoms 49 natoms 48 natoms 47 names: ZINC001580046826 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)COCC(F)F)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'F', 'F', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 15, 15, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 15, 15, 15, 26, 40, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 15, 26, 26, 50, 50, 50, 1, 1] 50 rigid atoms, others: [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 45, 46] set([37, 38, 39, 40, 41, 42, 43, 44, 14, 15, 16, 17, 18, 19, 20, 21, 22]) total number of confs: 181 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046826 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046826 Building ZINC001580046853 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046853 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 795) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/795 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/795' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046853 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 12, 12, 12, 12, 45, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 44, 44, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 796) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/796 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/796' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046853 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 11, 14, 14, 14, 46, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 14, 45, 45, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046853 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 Building ZINC001580046853 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046853 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 795) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/795: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046853.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046853 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 12, 12, 12, 12, 45, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 12, 44, 44, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 196 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 796) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/796: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046853.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046853.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046853 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 11, 14, 14, 14, 46, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 14, 45, 45, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046853 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046853 Building ZINC001580046854 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046854 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 797) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/797 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/797' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046854 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 12, 15, 15, 15, 47, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 15, 45, 45, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 798) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/798 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/798' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046854 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 13, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046854 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 Building ZINC001580046854 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046854 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 797) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/797: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046854.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046854 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 12, 15, 15, 15, 47, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 15, 45, 45, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 798) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/798: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046854.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046854.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046854 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 13, 13, 13, 13, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 13, 13, 13, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046854 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046854 Building ZINC001580046855 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046855 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 799) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/799 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/799' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046855 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 12, 15, 15, 15, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 15, 44, 44, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 800) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/800 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/800' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046855 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 11, 11, 11, 11, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046855 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 Building ZINC001580046855 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046855 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 799) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046855.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046855 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 12, 15, 15, 15, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 12, 12, 15, 44, 44, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 197 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 800) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1) `ZINC001580046855.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046855.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046855 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@@H](CNC(=O)C[C@@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 11, 11, 11, 11, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 11, 11, 11, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046855 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046855 Building ZINC001580046856 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046856 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 801) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/801 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/801' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046856 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 10, 10, 10, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 802) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/802 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/802' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046856 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 9, 13, 13, 13, 43, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 13, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046856 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 Building ZINC001580046856 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580046856 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 801) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046856.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580046856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046856 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 10, 10, 10, 10, 44, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 10, 10, 10, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 194 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 802) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1) `ZINC001580046856.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580046856.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580046856 none CC(C)(C)[C@]([O-])([SiH3])C(=O)N1CC[C@H](CNC(=O)C[C@H]2CCC(=O)N2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 5, 7, 5, 5, 1, 11, 8, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 7, 7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 3, 4, 5, 5, 5, 5, 5, 9, 13, 13, 13, 43, 50, 50, 50, 50, 50, 50, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 5, 5, 9, 9, 13, 43, 43, 50, 50, 50, 50, 50, 5, 5] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50]) total number of confs: 193 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580046856 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580046856 Building ZINC001580047133 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047133 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 803) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/803 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/803' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047133 none CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 39, 40, 10, 10, 10, 8, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 45, 47, 45, 45, 40, 40, 10, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 804) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/804 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/804' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047133 none CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 36, 15, 15, 15, 9, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 43, 46, 44, 44, 36, 36, 15, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047133 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 Building ZINC001580047133 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047133 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 803) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047133.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047133 none CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 39, 40, 10, 10, 10, 8, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 45, 47, 45, 45, 40, 40, 10, 8, 8, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 244 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 804) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047133.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047133.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047133 none CNC(=O)CCCC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 37, 36, 15, 15, 15, 9, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 43, 46, 44, 44, 36, 36, 15, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 243 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047133 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047133 Building ZINC001580047134 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047134 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 805) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/805 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/805' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047134 none CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 36, 15, 15, 15, 10, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 45, 43, 43, 43, 36, 36, 15, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 806) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/806 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/806' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047134 none CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 40, 41, 11, 11, 11, 9, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 47, 46, 45, 45, 41, 41, 11, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047134 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 Building ZINC001580047134 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047134 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 805) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047134.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047134 none CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 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, 35, 36, 15, 15, 15, 10, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 45, 43, 43, 43, 36, 36, 15, 10, 10, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 247 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 806) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580047134.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047134.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580047134 none CNC(=O)CCCC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 5, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 49, 50, 40, 41, 11, 11, 11, 9, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 49, 47, 46, 45, 45, 41, 41, 11, 9, 9, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 239 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047134 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047134 Building ZINC001580047387 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047387 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 807) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/807 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/807' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047387 none CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 47, 49, 47, 47, 23, 11, 11, 11, 11, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 49, 50, 50, 50, 50, 50, 50, 50, 47, 23, 23, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 808) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/808 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/808' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047387 none CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 45, 41, 41, 25, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 2, 2, 2, 14, 45, 49, 49, 50, 50, 50, 50, 50, 41, 25, 25, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047387 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 Building ZINC001580047387 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047387 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 807) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/807: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047387.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047387 none CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 47, 49, 47, 47, 23, 11, 11, 11, 11, 11, 4, 1, 7, 1, 1, 1, 1, 1, 1, 11, 49, 50, 50, 50, 50, 50, 50, 50, 47, 23, 23, 11, 11, 11, 11, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 160 number of broken/clashed sets: 5 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 808) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/808: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047387.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047387.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047387 none CC[C@H](C(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 41, 45, 41, 41, 25, 14, 14, 14, 14, 14, 4, 1, 8, 1, 1, 1, 2, 2, 2, 14, 45, 49, 49, 50, 50, 50, 50, 50, 41, 25, 25, 14, 14, 14, 14, 2, 2, 2, 2, 2, 2, 2, 2, 2, 14, 14, 49, 49, 49, 49, 49, 49] 50 rigid atoms, others: [16, 17, 13, 15] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 199 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047387 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047387 Building ZINC001580047390 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047390 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 809) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/809 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/809' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047390 none CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 46, 43, 43, 26, 12, 12, 12, 12, 12, 4, 1, 7, 1, 1, 1, 1, 1, 1, 12, 46, 50, 50, 50, 50, 50, 50, 50, 43, 26, 26, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 810) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/810 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/810' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047390 none CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 48, 44, 44, 21, 8, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 48, 50, 50, 50, 50, 50, 50, 50, 44, 21, 21, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047390 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 Building ZINC001580047390 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047390 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 809) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047390.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047390 none CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 43, 46, 43, 43, 26, 12, 12, 12, 12, 12, 4, 1, 7, 1, 1, 1, 1, 1, 1, 12, 46, 50, 50, 50, 50, 50, 50, 50, 43, 26, 26, 12, 12, 12, 12, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 12, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 810) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C) `ZINC001580047390.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047390.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 15 0 4 15 1 4 15 2 3 15 2 18 to be deleted 19 to be deleted 20 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580047390 none CC[C@H](C(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)N(C)C NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 7, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 10, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 44, 48, 44, 44, 21, 8, 8, 8, 8, 8, 3, 1, 5, 1, 1, 1, 1, 1, 1, 8, 48, 50, 50, 50, 50, 50, 50, 50, 44, 21, 21, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047390 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047390 Building ZINC001580047895 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047895 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 811) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/811 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/811' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047895 none C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 30, 30, 30, 17, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 48, 48, 30, 17, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 812) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/812 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/812' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047895 none C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 29, 29, 29, 15, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 47, 47, 29, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047895 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 Building ZINC001580047895 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047895 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 811) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047895.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047895 none C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 30, 30, 30, 17, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 48, 48, 30, 17, 17, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 812) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047895.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047895.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047895 none C[C@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 29, 29, 29, 15, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 47, 47, 29, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 211 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047895 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047895 Building ZINC001580047896 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047896 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 813) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/813 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/813' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047896 none C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 26, 26, 16, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 16, 16, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 814) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/814 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/814' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047896 none C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 29, 29, 29, 15, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 49, 49, 29, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047896 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 Building ZINC001580047896 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047896 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 813) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047896.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047896 none C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 26, 26, 16, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 16, 16, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 210 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 814) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047896.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047896.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047896 none C[C@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 29, 29, 29, 15, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 49, 49, 29, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047896 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047896 Building ZINC001580047897 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047897 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 815) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/815 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/815' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047897 none C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 30, 30, 30, 17, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 47, 47, 30, 17, 17, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 816) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/816 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/816' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047897 none C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 27, 27, 27, 15, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 48, 48, 27, 15, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047897 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 Building ZINC001580047897 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047897 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 815) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047897.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047897 none C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 30, 30, 30, 17, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 47, 47, 30, 17, 17, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 816) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047897.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047897.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047897 none C[C@@H](CC(=O)NC[C@@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 48, 50, 27, 27, 27, 15, 5, 5, 5, 5, 5, 3, 1, 4, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 48, 48, 27, 15, 15, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047897 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047897 Building ZINC001580047898 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047898 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 817) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/817 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/817' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047898 none C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 29, 29, 29, 15, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 49, 49, 29, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 818) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/818 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/818' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047898 none C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 26, 26, 14, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047898 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 Building ZINC001580047898 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580047898 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 817) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/817: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047898.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580047898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047898 none C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 49, 50, 29, 29, 29, 15, 4, 4, 4, 4, 4, 3, 1, 4, 1, 1, 1, 1, 1, 1, 4, 50, 50, 50, 50, 50, 50, 50, 49, 49, 29, 15, 15, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 198 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 818) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/818: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580047898.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580047898.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580047898 none C[C@@H](CC(=O)NC[C@H]1CCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 26, 26, 26, 14, 5, 5, 5, 5, 5, 3, 1, 5, 1, 1, 1, 1, 1, 1, 5, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 14, 14, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580047898 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580047898 Building ZINC001580072750 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580072750 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 819) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/819 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/819' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)c1) `ZINC001580072750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580072750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580072750 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 44, 44, 44, 44, 44, 50, 50, 50, 50, 50, 44, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 820) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/820 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/820' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)c1) `ZINC001580072750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580072750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580072750 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580072750 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 Building ZINC001580072750 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580072750 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 819) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)c1) `ZINC001580072750.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580072750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580072750 none COc1ccccc1[C@@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 44, 44, 44, 44, 44, 50, 50, 50, 50, 50, 44, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 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: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 820) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)c1) `ZINC001580072750.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580072750.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580072750 none COc1ccccc1[C@]([O-])([SiH3])C(=O)NCc1ccnc(c2nn[nH]n2)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.ar', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', '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, 1, 1, 5, 12, 1, 11, 8, 5, 1, 1, 1, 8, 1, 1, 8, 8, 8, 6, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 3, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 15, 46, 46, 46, 46, 46, 50, 50, 50, 50, 50, 46, 2, 2, 2, 2, 2, 2, 2, 3, 15, 15, 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]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580072750 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580072750 Building ZINC001580088252 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088252 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 821) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/821 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/821' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088252 none C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 27, 26, 27, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 822) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/822 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/822' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088252 none C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 25, 25, 25, 25, 25, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088252 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 Building ZINC001580088252 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088252 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 821) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/821: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088252.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088252 none C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 27, 26, 27, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 822) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/822: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088252.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088252.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088252 none C[C@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 25, 25, 25, 25, 25, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088252 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088252 Building ZINC001580088253 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088253 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 823) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/823 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/823' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088253 none C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 21, 21, 21, 21, 21, 21, 14, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 49, 50, 50, 50, 49, 49, 49, 46, 46, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 824) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/824 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/824' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088253 none C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 21, 21, 21, 21, 21, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088253 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 Building ZINC001580088253 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088253 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 823) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088253.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088253 none C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 21, 21, 21, 21, 21, 21, 14, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 49, 50, 50, 50, 49, 49, 49, 46, 46, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 824) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088253.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088253.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088253 none C[C@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 21, 21, 21, 21, 21, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088253 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088253 Building ZINC001580088254 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088254 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 825) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/825 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/825' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088254 none C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 25, 25, 25, 25, 25, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 826) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/826 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/826' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088254 none C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 27, 26, 27, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088254 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 Building ZINC001580088254 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088254 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 825) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088254.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088254 none C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 45, 50, 25, 25, 25, 25, 25, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 50, 50, 50, 50, 50, 50, 50, 45, 45, 25, 25, 25, 25, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 826) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088254.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088254.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088254 none C[C@@H](CC(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 47, 50, 27, 26, 27, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 47, 47, 26, 26, 26, 26, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088254 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088254 Building ZINC001580088255 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088255 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 827) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/827 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/827' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088255 none C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 21, 21, 21, 21, 21, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 828) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/828 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/828' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088255 none C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 21, 21, 21, 21, 21, 21, 14, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 49, 50, 50, 50, 49, 49, 49, 46, 46, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088255 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 Building ZINC001580088255 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580088255 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 827) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088255.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580088255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088255 none C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 46, 50, 21, 21, 21, 21, 21, 21, 11, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 50, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 21, 21, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 828) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O) `ZINC001580088255.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580088255.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580088255 none C[C@@H](CC(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1)NC(N)=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'N.am', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 1, 8, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6] dock color type numbers: [7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [49, 46, 49, 21, 21, 21, 21, 21, 21, 14, 21, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 21, 49, 50, 50, 50, 49, 49, 49, 46, 46, 21, 21, 21, 21, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 50, 50, 50] 50 rigid atoms, others: [45, 38, 39, 40, 41, 42, 43, 44, 13, 46, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48, 49, 50, 51]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580088255 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580088255 Building ZINC001580092625 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580092625 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 829) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/829 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/829' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580092625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092625 none Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 38, 37, 37, 37, 17, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 830) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/830 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/830' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580092625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092625 none Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 38, 37, 37, 37, 18, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580092625 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 Building ZINC001580092625 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580092625 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 829) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092625.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580092625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092625 none Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 38, 37, 37, 37, 17, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 830) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092625.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580092625.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092625 none Cc1nccc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 38, 37, 37, 37, 18, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580092625 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092625 Building ZINC001580092626 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580092626 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 831) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/831 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/831' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580092626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092626 none Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 36, 37, 36, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 832) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/832 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/832' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580092626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092626 none Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 38, 37, 37, 37, 17, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580092626 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 Building ZINC001580092626 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580092626 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 831) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092626.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580092626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092626 none Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 37, 36, 37, 36, 36, 36, 18, 36, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 50, 50, 50, 50, 50, 50, 36, 36, 36, 36, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 36, 36] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 832) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580092626.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580092626.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580092626 none Cc1nccc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 38, 37, 38, 37, 37, 37, 17, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 50, 37, 37, 37, 37, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 15, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580092626 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580092626 Building ZINC001580120793 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580120793 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 833) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/833 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/833' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580120793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120793 none CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 50, 50, 50, 50, 50, 33, 33, 33, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 834) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/834 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/834' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580120793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120793 none CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 16, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 50, 50, 50, 50, 50, 38, 38, 38, 29, 29, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580120793 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 Building ZINC001580120793 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580120793 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 833) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/833: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120793.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580120793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120793 none CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 50, 50, 50, 50, 50, 33, 33, 33, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 834) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/834: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120793.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580120793.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120793 none CCn1nc(C)c(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 16, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 50, 50, 50, 50, 50, 38, 38, 38, 29, 29, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580120793 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120793 Building ZINC001580120794 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580120794 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 835) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/835 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/835' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580120794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120794 none CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 16, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 50, 50, 50, 50, 50, 38, 38, 38, 29, 29, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 836) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/836 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/836' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580120794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120794 none CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 50, 50, 50, 50, 50, 33, 33, 33, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580120794 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 Building ZINC001580120794 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580120794 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 835) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120794.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580120794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120794 none CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 29, 29, 29, 29, 29, 29, 16, 29, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 29, 38, 50, 50, 50, 50, 50, 38, 38, 38, 29, 29, 29, 29, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 29, 29] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 836) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580120794.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580120794.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580120794 none CCn1nc(C)c(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.3', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 5, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 33, 26, 26, 26, 26, 26, 26, 13, 26, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 33, 50, 50, 50, 50, 50, 33, 33, 33, 26, 26, 26, 26, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 26] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580120794 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580120794 Building ZINC001580130843 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580130843 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 837) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/837 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/837' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580130843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130843 none Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 35, 36, 35, 35, 35, 15, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 838) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/838 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/838' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580130843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130843 none Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 37, 39, 37, 37, 37, 19, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580130843 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 Building ZINC001580130843 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580130843 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 837) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130843.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580130843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130843 none Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 35, 36, 35, 35, 35, 15, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 838) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130843.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580130843.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130843 none Cc1nnccc1C(=O)N1CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 37, 39, 37, 37, 37, 19, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580130843 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130843 Building ZINC001580130844 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580130844 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 839) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/839 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/839' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580130844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130844 none Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 37, 39, 37, 37, 37, 19, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 840) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/840 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/840' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580130844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130844 none Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 35, 36, 35, 35, 35, 15, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580130844 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 Building ZINC001580130844 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580130844 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 839) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130844.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580130844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130844 none Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 37, 39, 37, 37, 37, 19, 37, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 37, 50, 50, 50, 50, 50, 37, 37, 37, 37, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 37, 37] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 134 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 840) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580130844.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580130844.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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: ZINC001580130844 none Cc1nnccc1C(=O)N1CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.ar', 'N.ar', 'N.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 8, 1, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 3, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 36, 35, 36, 35, 35, 35, 15, 35, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 35, 35, 35, 35, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 35, 35] 50 rigid atoms, others: [37, 38, 39, 40, 41, 42, 43, 44, 45, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580130844 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580130844 Building ZINC001580132211 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132211 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 841) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/841 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/841' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132211 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 26, 26, 26, 27, 27, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 842) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/842 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/842' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132211 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 26, 26, 26, 26, 26, 27, 27, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132211 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 Building ZINC001580132211 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132211 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 841) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132211.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132211 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 26, 26, 26, 26, 26, 27, 27, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 118 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 842) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132211.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132211.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132211 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 26, 26, 26, 26, 26, 27, 27, 50, 50, 50, 50, 50, 50, 50, 26, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 26, 26, 26, 26, 50, 50, 50, 50, 26, 26] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 107 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132211 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132211 Building ZINC001580132212 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132212 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 843) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/843 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/843' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132212 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 25, 25, 25, 25, 25, 26, 26, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 844) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/844 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/844' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132212 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 25, 25, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132212 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 Building ZINC001580132212 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132212 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 843) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/843: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132212.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132212 none CC(C)(C)[C@@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 25, 25, 25, 25, 25, 26, 26, 50, 50, 50, 50, 50, 50, 50, 25, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 25, 25, 25, 25, 50, 50, 50, 50, 25, 25] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 8, 9, 5, 34, 35, 7, 26, 27, 28, 29, 30, 31] set([10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 108 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 844) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/844: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1) `ZINC001580132212.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132212.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580132212 none CC(C)(C)[C@]([O-])([SiH3])C(=O)NC[C@H]1CCN(C(=O)c2coc(C(N)=O)c2)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'O.3', 'C.2', 'C.2', 'N.am', 'O.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 5, 5, 12, 1, 11, 8, 5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 12, 1, 1, 8, 11, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7] dock color type numbers: [7, 9, 7, 7, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 3, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 13, 24, 24, 24, 24, 24, 25, 25, 50, 50, 50, 50, 50, 50, 50, 24, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 8, 8, 24, 24, 24, 24, 50, 50, 50, 50, 24, 24] 50 rigid atoms, others: [0, 1, 2, 3, 4, 33, 6, 32, 5, 34, 26, 27, 28, 29, 30, 31] set([7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47]) total number of confs: 115 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132212 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132212 Building ZINC001580132339 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132339 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 845) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/845 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/845' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132339 none COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 41, 43, 41, 41, 41, 18, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 846) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/846 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/846' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132339 none COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 40, 42, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 40, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132339 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 Building ZINC001580132339 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132339 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 845) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132339.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132339 none COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 43, 41, 43, 41, 41, 41, 18, 41, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 41, 50, 50, 50, 50, 50, 41, 41, 41, 41, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 41, 41, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 139 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 846) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132339.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132339.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132339 none COc1nc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 40, 42, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 40, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132339 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132339 Building ZINC001580132340 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132340 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 847) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/847 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/847' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132340 none COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 40, 42, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 40, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 848) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/848 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/848' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132340 none COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 42, 44, 42, 42, 42, 17, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132340 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 Building ZINC001580132340 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580132340 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 847) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132340.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580132340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132340 none COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 42, 40, 42, 40, 40, 40, 17, 40, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 40, 40, 40, 40, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 40, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 136 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 848) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1) `ZINC001580132340.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580132340.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580132340 none COc1nc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)co1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'N.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.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, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 1, 12, 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, 3, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 44, 42, 44, 42, 42, 42, 17, 42, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50, 50, 42, 42, 42, 42, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 42, 50] 50 rigid atoms, others: [35, 36, 37, 38, 39, 40, 41, 42, 43, 14, 16, 17, 18, 19, 20, 21] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 44, 45, 46]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580132340 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580132340 Building ZINC001580159150 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159150 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 849) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/849 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/849' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159150 none CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 32, 28, 32, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 35, 35, 50, 50, 50, 50, 50, 35, 28, 28, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 850) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/850 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/850' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159150 none CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 29, 28, 29, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 35, 35, 50, 50, 50, 50, 50, 35, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159150 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 Building ZINC001580159150 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159150 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 849) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159150.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159150 none CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 32, 28, 32, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 35, 35, 50, 50, 50, 50, 50, 35, 28, 28, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 186 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 850) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159150.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159150.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159150 none CCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 29, 28, 29, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 35, 35, 50, 50, 50, 50, 50, 35, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159150 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159150 Building ZINC001580159151 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159151 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 851) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/851 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/851' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159151 none CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 29, 28, 29, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 35, 35, 50, 50, 50, 50, 50, 35, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 852) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/852 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/852' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159151 none CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 31, 28, 31, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 34, 34, 50, 50, 50, 50, 50, 34, 28, 28, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159151 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 Building ZINC001580159151 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159151 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 851) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159151.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159151 none CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 35, 29, 28, 29, 28, 28, 28, 16, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 35, 35, 50, 50, 50, 50, 50, 35, 28, 28, 28, 28, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 852) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159151.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159151.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580159151 none CCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 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, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 34, 34, 34, 31, 28, 31, 28, 28, 28, 15, 28, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 34, 34, 50, 50, 50, 50, 50, 34, 28, 28, 28, 28, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 28, 28] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159151 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159151 Building ZINC001580159990 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159990 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 853) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/853 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/853' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159990 none CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 25, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 854) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/854 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/854' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159990 none CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 25, 24, 25, 24, 24, 24, 14, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 24, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159990 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 Building ZINC001580159990 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159990 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 853) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159990.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159990 none CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 25, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 854) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159990.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159990.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159990 none CCCn1cc(C(=O)N2CC[C@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 25, 24, 25, 24, 24, 24, 14, 24, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 24, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 24, 24, 24, 24, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 24] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159990 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159990 Building ZINC001580159992 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159992 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 855) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/855 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/855' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159992 none CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 25, 25, 25, 25, 25, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 25, 25, 25, 25, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 856) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/856 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/856' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159992 none CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 25, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159992 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 Building ZINC001580159992 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580159992 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 855) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159992.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580159992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159992 none CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 32, 32, 32, 25, 25, 25, 25, 25, 25, 15, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 32, 32, 50, 50, 50, 50, 50, 50, 50, 32, 25, 25, 25, 25, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 856) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1) `ZINC001580159992.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580159992.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580159992 none CCCn1cc(C(=O)N2CC[C@@H](CNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 33, 33, 33, 25, 25, 25, 25, 25, 25, 14, 25, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 33, 33, 50, 50, 50, 50, 50, 50, 50, 33, 25, 25, 25, 25, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580159992 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580159992 Building ZINC001580227120 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227120 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 857) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/857 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/857' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227120 none CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 41, 50, 50, 50, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 41, 41, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 198 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 858) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/858 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/858' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227120 none CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 16, 16, 37, 50, 50, 50, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 37, 37, 50, 50, 50, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227120 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 Building ZINC001580227120 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227120 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 857) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227120.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227120 none CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 17, 17, 41, 50, 50, 50, 4, 4, 4, 4, 4, 4, 2, 4, 1, 1, 1, 1, 1, 1, 4, 6, 6, 6, 41, 41, 50, 50, 50, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 198 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 858) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227120.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227120.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227120 none CN(C(=O)CS(C)(=O)=O)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 3, 5, 16, 16, 37, 50, 50, 50, 3, 3, 3, 3, 3, 3, 2, 3, 1, 1, 1, 1, 1, 1, 3, 5, 5, 5, 37, 37, 50, 50, 50, 3, 3, 3, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 3, 3] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 219 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227120 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227120 Building ZINC001580227121 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227121 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 859) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/859 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/859' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227121 none CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 41, 50, 50, 50, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 41, 41, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 195 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 860) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/860 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/860' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227121 none CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 43, 50, 50, 50, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 43, 43, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 196 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227121 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 Building ZINC001580227121 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227121 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 859) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227121.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227121 none CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 41, 50, 50, 50, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 41, 41, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 195 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 860) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227121.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227121.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580227121 none CN(C(=O)CS(C)(=O)=O)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'S.o2', 'C.3', 'O.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 14, 5, 11, 11, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 6, 7, 7, 7, 3, 3, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 18, 43, 50, 50, 50, 6, 6, 6, 6, 6, 6, 2, 6, 1, 1, 1, 1, 1, 1, 6, 7, 7, 7, 43, 43, 50, 50, 50, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 46, 17, 18, 19, 20, 21, 22] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47, 48]) total number of confs: 196 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227121 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227121 Building ZINC001580227602 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227602 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 861) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/861 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/861' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227602 none C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 41, 41, 48, 50, 50, 16, 32, 9, 16, 9, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 1, 1, 1, 9, 41, 41, 41, 48, 48, 50, 50, 16, 16, 16, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 198 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 862) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/862 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/862' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227602 none C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 32, 32, 45, 50, 50, 10, 24, 6, 10, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 32, 32, 32, 45, 45, 50, 50, 10, 10, 10, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 204 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227602 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 Building ZINC001580227602 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227602 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 861) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227602.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227602 none C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 32, 41, 41, 48, 50, 50, 16, 32, 9, 16, 9, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 1, 1, 1, 9, 41, 41, 41, 48, 48, 50, 50, 16, 16, 16, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 198 number of broken/clashed sets: 14 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 862) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227602.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227602.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227602 none C[C@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 24, 32, 32, 45, 50, 50, 10, 24, 6, 10, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 32, 32, 32, 45, 45, 50, 50, 10, 10, 10, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 204 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227602 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227602 Building ZINC001580227603 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227603 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 863) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/863 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/863' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227603 none C[C@@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 36, 48, 50, 50, 12, 25, 4, 12, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 36, 36, 36, 48, 48, 50, 50, 12, 12, 12, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 207 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 864) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/864 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/864' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227603 none C[C@@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 37, 37, 46, 50, 50, 16, 29, 7, 16, 7, 7, 7, 7, 7, 4, 2, 7, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 46, 46, 50, 50, 16, 16, 16, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 196 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227603 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 Building ZINC001580227603 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227603 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 863) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227603.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227603 none C[C@@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 25, 36, 36, 48, 50, 50, 12, 25, 4, 12, 4, 4, 4, 4, 4, 3, 2, 4, 1, 1, 1, 1, 1, 1, 4, 36, 36, 36, 48, 48, 50, 50, 12, 12, 12, 4, 4, 4, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 4, 4] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 207 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 864) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227603.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227603.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227603 none C[C@@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 29, 37, 37, 46, 50, 50, 16, 29, 7, 16, 7, 7, 7, 7, 7, 4, 2, 7, 1, 1, 1, 1, 1, 1, 7, 37, 37, 37, 46, 46, 50, 50, 16, 16, 16, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 196 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227603 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227603 Building ZINC001580227604 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227604 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 865) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/865 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/865' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227604 none C[C@@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 35, 35, 49, 50, 50, 14, 26, 9, 14, 9, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 49, 49, 50, 50, 14, 14, 14, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 204 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 866) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/866 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/866' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227604 none C[C@@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 35, 35, 47, 50, 50, 11, 24, 6, 11, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 35, 35, 35, 47, 47, 50, 50, 11, 11, 11, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227604 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 Building ZINC001580227604 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227604 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 865) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227604.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227604 none C[C@@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 26, 35, 35, 49, 50, 50, 14, 26, 9, 14, 9, 9, 9, 9, 9, 6, 2, 6, 1, 1, 1, 1, 1, 1, 9, 35, 35, 35, 49, 49, 50, 50, 14, 14, 14, 9, 9, 9, 9, 9, 9, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 204 number of broken/clashed sets: 11 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 866) grep: /scratch/xiaobo/167320/xcr-8058097.70/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](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227604.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227604.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227604 none C[C@@H](CC(N)=O)C(=O)N(C)[C@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 24, 35, 35, 47, 50, 50, 11, 24, 6, 11, 6, 6, 6, 6, 6, 4, 2, 4, 1, 1, 1, 1, 1, 1, 6, 35, 35, 35, 47, 47, 50, 50, 11, 11, 11, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 202 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227604 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227604 Building ZINC001580227605 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227605 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 867) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/867 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/867' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227605 none C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 34, 34, 46, 50, 50, 12, 22, 5, 12, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 34, 34, 34, 46, 46, 50, 50, 12, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 868) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/868 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/868' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227605 none C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 48, 50, 50, 15, 28, 8, 15, 8, 8, 8, 8, 8, 5, 2, 8, 1, 1, 1, 1, 1, 1, 8, 39, 39, 39, 48, 48, 50, 50, 15, 15, 15, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227605 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 Building ZINC001580227605 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580227605 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 867) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227605.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580227605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227605 none C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 34, 34, 46, 50, 50, 12, 22, 5, 12, 5, 5, 5, 5, 5, 4, 2, 5, 1, 1, 1, 1, 1, 1, 5, 34, 34, 34, 46, 46, 50, 50, 12, 12, 12, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 1, 1, 1, 1, 1, 5, 5] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 203 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 868) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580227605.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580227605.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580227605 none C[C@H](CC(N)=O)C(=O)N(C)[C@@H]1CCCN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.2', 'N.am', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 1, 8, 11, 1, 11, 8, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 39, 39, 48, 50, 50, 15, 28, 8, 15, 8, 8, 8, 8, 8, 5, 2, 8, 1, 1, 1, 1, 1, 1, 8, 39, 39, 39, 48, 48, 50, 50, 15, 15, 15, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [42, 43, 44, 45, 46, 47, 48, 49, 50, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 194 number of broken/clashed sets: 10 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580227605 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580227605 Building ZINC001580234452 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580234452 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 869) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/869 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/869' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580234452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234452 none CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 33, 10, 7, 10, 7, 7, 7, 7, 3, 7, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 33, 27, 27, 7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 870) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/870 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/870' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580234452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234452 none CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 36, 12, 6, 12, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 36, 24, 24, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51, 52]) total number of confs: 205 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580234452 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 Building ZINC001580234452 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580234452 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 869) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580234452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234452 none CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 27, 33, 10, 7, 10, 7, 7, 7, 7, 3, 7, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 7, 50, 50, 50, 50, 50, 33, 27, 27, 7, 7, 7, 7, 7, 7, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 225 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 870) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580234452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234452 none CCNC(=O)CC(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 24, 36, 12, 6, 12, 6, 6, 6, 6, 1, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 50, 50, 50, 50, 50, 36, 24, 24, 6, 6, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6] 50 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51, 52]) total number of confs: 205 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580234452 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234452 Building ZINC001580234453 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580234453 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 871) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/871 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/871' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580234453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234453 none CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 25, 35, 17, 8, 17, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 35, 25, 25, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51, 52]) total number of confs: 211 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 872) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/872 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/872' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580234453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234453 none CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 24, 32, 17, 9, 17, 9, 9, 9, 9, 3, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 32, 24, 24, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580234453 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 Building ZINC001580234453 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580234453 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 871) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234453.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580234453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234453 none CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 35, 35, 25, 35, 17, 8, 17, 8, 8, 8, 8, 2, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 35, 25, 25, 8, 8, 8, 8, 8, 8, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 51, 52]) total number of confs: 211 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 872) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580234453.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580234453.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580234453 none CCNC(=O)CC(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 1, 11, 5, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 4, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 24, 32, 17, 9, 17, 9, 9, 9, 9, 3, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 32, 24, 24, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 216 number of broken/clashed sets: 9 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580234453 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580234453 Building ZINC001580237890 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580237890 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 873) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/873 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/873' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580237890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237890 none CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 30, 11, 30, 11, 11, 11, 11, 2, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 33, 50, 50, 50, 50, 50, 33, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 874) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/874 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/874' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580237890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237890 none CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 27, 7, 27, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 50, 50, 50, 50, 50, 37, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580237890 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 Building ZINC001580237890 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580237890 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 873) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237890.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580237890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237890 none CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 33, 33, 33, 33, 30, 11, 30, 11, 11, 11, 11, 2, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 33, 50, 50, 50, 50, 50, 33, 11, 11, 11, 11, 11, 11, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 874) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237890.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580237890.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237890 none CCn1ncc(C(=O)N2CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 27, 7, 27, 7, 7, 7, 7, 1, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 37, 50, 50, 50, 50, 50, 37, 7, 7, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 7, 7] 50 rigid atoms, others: [12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 13, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580237890 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237890 Building ZINC001580237891 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580237891 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 875) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/875 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/875' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580237891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237891 none CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 29, 11, 29, 11, 11, 11, 11, 3, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 37, 50, 50, 50, 50, 50, 37, 11, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 876) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/876 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/876' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580237891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237891 none CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 25, 10, 25, 10, 10, 10, 10, 2, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 32, 50, 50, 50, 50, 50, 32, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580237891 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 Building ZINC001580237891 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580237891 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 875) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237891.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580237891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237891 none CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 37, 37, 37, 37, 29, 11, 29, 11, 11, 11, 11, 3, 11, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 11, 37, 50, 50, 50, 50, 50, 37, 11, 11, 11, 11, 11, 11, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 11] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 876) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1) `ZINC001580237891.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580237891.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580237891 none CCn1ncc(C(=O)N2CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C2)n1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 32, 32, 32, 32, 25, 10, 25, 10, 10, 10, 10, 2, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 32, 50, 50, 50, 50, 50, 32, 10, 10, 10, 10, 10, 10, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [48, 41, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580237891 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580237891 Building ZINC001580239116 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580239116 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 877) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/877 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/877' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580239116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239116 none CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 43, 43, 43, 43, 26, 9, 26, 9, 9, 9, 9, 3, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 43, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 878) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/878 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/878' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580239116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239116 none CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 28, 8, 28, 8, 8, 8, 8, 3, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 39, 8, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580239116 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 Building ZINC001580239116 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580239116 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 877) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239116.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580239116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239116 none CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 43, 43, 43, 43, 43, 26, 9, 26, 9, 9, 9, 9, 3, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 43, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 143 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 878) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239116.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580239116.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239116 none CCn1nncc1C(=O)N1CCC[C@@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 28, 8, 28, 8, 8, 8, 8, 3, 8, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 8, 50, 50, 50, 50, 50, 39, 8, 8, 8, 8, 8, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 161 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580239116 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239116 Building ZINC001580239117 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580239117 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 879) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/879 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/879' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580239117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239117 none CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 21, 10, 21, 10, 10, 10, 10, 4, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 39, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 880) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/880 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/880' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580239117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239117 none CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 22, 9, 22, 9, 9, 9, 9, 3, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 38, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580239117 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 Building ZINC001580239117 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580239117 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 879) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239117.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580239117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239117 none CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 39, 39, 39, 39, 39, 21, 10, 21, 10, 10, 10, 10, 4, 10, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 10, 50, 50, 50, 50, 50, 39, 10, 10, 10, 10, 10, 10, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 10] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 880) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580239117.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580239117.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580239117 none CCn1nncc1C(=O)N1CCC[C@H](N(C)C(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'N.pl3', 'N.2', 'N.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 8, 8, 8, 1, 1, 1, 11, 8, 5, 5, 5, 5, 7, 8, 5, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 38, 38, 38, 38, 38, 22, 9, 22, 9, 9, 9, 9, 3, 9, 2, 3, 1, 2, 1, 1, 1, 1, 1, 1, 9, 50, 50, 50, 50, 50, 38, 9, 9, 9, 9, 9, 9, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9] 50 rigid atoms, others: [49, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 50, 51]) total number of confs: 164 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580239117 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580239117 Building ZINC001580243317 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580243317 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 881) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/881 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/881' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580243317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243317 none NC[C@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 12, 12, 25, 12, 12, 12, 12, 7, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 25, 25, 75, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 882) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/882 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/882' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580243317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243317 none NC[C@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 12, 28, 12, 12, 12, 12, 8, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 28, 28, 84, 12, 12, 12, 12, 12, 12, 8, 8, 8, 8] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 267 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580243317 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 Building ZINC001580243317 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580243317 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 881) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: NC[C@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580243317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243317 none NC[C@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens need rotated 150 conformations in input total number of sets (complete confs): 150 using faster count positions algorithm for large data unique positions, atoms: [22, 12, 12, 12, 25, 12, 12, 12, 12, 7, 2, 10, 1, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 22, 22, 22, 22, 25, 25, 75, 12, 12, 12, 12, 12, 12, 7, 7, 7, 7] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 218 number of broken/clashed sets: 44 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 882) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: NC[C@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580243317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243317 none NC[C@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 12, 12, 12, 28, 12, 12, 12, 12, 8, 2, 10, 1, 1, 1, 8, 8, 8, 8, 8, 8, 8, 8, 8, 8, 25, 25, 25, 25, 28, 28, 84, 12, 12, 12, 12, 12, 12, 8, 8, 8, 8] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 267 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580243317 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243317 Building ZINC001580243318 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580243318 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 883) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/883 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/883' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580243318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243318 none NC[C@@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 15, 28, 15, 15, 15, 15, 9, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 28, 84, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 249 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 884) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/884 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/884' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: NC[C@@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580243318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243318 none NC[C@@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 11, 31, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 31, 31, 93, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 289 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580243318 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 Building ZINC001580243318 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580243318 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 883) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: NC[C@@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243318.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580243318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243318 none NC[C@@]1(CO)COCCN1C(=O)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 15, 15, 15, 28, 15, 15, 15, 15, 9, 2, 12, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 27, 27, 27, 27, 28, 28, 84, 15, 15, 15, 15, 15, 15, 6, 6, 6, 6] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 249 number of broken/clashed sets: 50 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 884) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: NC[C@@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580243318.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580243318.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 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: ZINC001580243318 none NC[C@@]1(CO)COCCN1C(=O)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [10, 5, 5, 5, 12, 5, 12, 5, 5, 8, 1, 11, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 7, 3, 7, 7, 7, 9, 6, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 1 hydrogens 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, 11, 11, 11, 31, 11, 11, 11, 11, 6, 2, 8, 1, 1, 1, 6, 6, 6, 6, 6, 6, 6, 6, 6, 6, 28, 28, 28, 28, 31, 31, 93, 11, 11, 11, 11, 11, 11, 6, 6, 6, 6] 150 rigid atoms, others: [12, 13, 14] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 289 number of broken/clashed sets: 43 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580243318 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580243318 Building ZINC001580246996 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580246996 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 885) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/885 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/885' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580246996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246996 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 21, 38, 38, 41, 41, 41, 50, 50, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 41, 41, 41, 41, 41, 41, 50, 50, 21, 21] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 886) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/886 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/886' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580246996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246996 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 32, 32, 36, 36, 36, 50, 50, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 36, 36, 36, 36, 36, 36, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580246996 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 Building ZINC001580246996 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580246996 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 885) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246996.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580246996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246996 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 21, 21, 21, 21, 21, 21, 38, 38, 41, 41, 41, 50, 50, 21, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 21, 21, 21, 21, 21, 21, 41, 41, 41, 41, 41, 41, 50, 50, 21, 21] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 18 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 886) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246996.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580246996.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246996 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 17, 17, 17, 17, 17, 17, 32, 32, 36, 36, 36, 50, 50, 17, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 17, 17, 17, 17, 17, 17, 36, 36, 36, 36, 36, 36, 50, 50, 17, 17] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 177 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580246996 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246996 Building ZINC001580246998 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580246998 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 887) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/887 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/887' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580246998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246998 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 25, 25, 25, 25, 25, 25, 33, 33, 35, 35, 35, 50, 50, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 50, 50, 25, 25] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 888) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/888 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/888' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580246998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246998 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 30, 30, 30, 30, 30, 30, 37, 37, 38, 38, 38, 50, 50, 30, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 38, 38, 38, 38, 38, 38, 50, 50, 30, 30] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580246998 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 Building ZINC001580246998 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580246998 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 887) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246998.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580246998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246998 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 25, 25, 25, 25, 25, 25, 33, 33, 35, 35, 35, 50, 50, 25, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 25, 25, 25, 25, 25, 35, 35, 35, 35, 35, 35, 50, 50, 25, 25] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 13 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 888) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1) `ZINC001580246998.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580246998.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580246998 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)C(C)(C)C(N)=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.2', 'N.am', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 5, 5, 1, 8, 11, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 3, 1, 3, 1, 1, 1, 1, 1, 1, 4, 30, 30, 30, 30, 30, 30, 37, 37, 38, 38, 38, 50, 50, 30, 4, 4, 4, 1, 1, 1, 1, 1, 1, 1, 1, 1, 30, 30, 30, 30, 30, 30, 38, 38, 38, 38, 38, 38, 50, 50, 30, 30] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 19 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580246998 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580246998 Building ZINC001580248933 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580248933 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 889) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/889 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/889' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580248933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248933 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 13, 13, 30, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 30, 30, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 890) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/890 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/890' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580248933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248933 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 13, 13, 31, 50, 50, 50, 50, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 31, 31, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580248933 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 Building ZINC001580248933 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580248933 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 889) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248933.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580248933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248933 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 8, 8, 8, 8, 8, 8, 13, 13, 30, 50, 50, 50, 50, 8, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 30, 30, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 150 number of broken/clashed sets: 21 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 890) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248933.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580248933.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248933 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 1, 1, 3, 8, 8, 8, 8, 8, 8, 13, 13, 31, 50, 50, 50, 50, 8, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 8, 8, 8, 8, 8, 8, 31, 31, 50, 50, 50, 8, 8] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 159 number of broken/clashed sets: 17 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580248933 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248933 Building ZINC001580248934 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580248934 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 891) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/891 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/891' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580248934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248934 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 33, 50, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 33, 33, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 892) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/892 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/892' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580248934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248934 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 15, 15, 33, 50, 50, 50, 50, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 33, 33, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580248934 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 Building ZINC001580248934 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580248934 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 891) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248934.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580248934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248934 none CN(C(=O)[C@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 2, 1, 1, 1, 1, 1, 1, 3, 6, 6, 6, 6, 6, 6, 14, 14, 33, 50, 50, 50, 50, 6, 3, 3, 3, 1, 1, 1, 1, 1, 1, 1, 1, 1, 6, 6, 6, 6, 6, 6, 33, 33, 50, 50, 50, 6, 6] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 156 number of broken/clashed sets: 16 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 892) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1) `ZINC001580248934.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580248934.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 4 is the cov attach 4 4 0 4 4 1 4 4 2 3 4 2 7 to be deleted 8 to be deleted 9 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580248934 none CN(C(=O)[C@@]([O-])([SiH3])C(C)(C)C)[C@H]1CCCN(C(=O)Cn2ccnc2)C1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.pl3', 'C.2', 'C.2', 'N.2', 'C.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 8, 1, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 2, 9, 9, 9, 9, 9, 9, 15, 15, 33, 50, 50, 50, 50, 9, 2, 2, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 9, 9, 9, 9, 9, 9, 33, 33, 50, 50, 50, 9, 9] 50 rigid atoms, others: [32, 33, 2, 35, 4, 5, 6, 7, 8, 9, 34, 36, 28, 29, 30, 31] set([0, 1, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 149 number of broken/clashed sets: 15 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580248934 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580248934 Building ZINC001580317713 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317713 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 893) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/893 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/893' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O) `ZINC001580317713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317713 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 33, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 894) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/894 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/894' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O) `ZINC001580317713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317713 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317713 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 Building ZINC001580317713 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317713 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 893) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O) `ZINC001580317713.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317713 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [33, 17, 33, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 48, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 894) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O) `ZINC001580317713.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317713.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317713 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cn(C)ccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 5, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 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 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 16, 32, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317713 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317713 Building ZINC001580317763 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317763 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 895) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/895 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/895' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12) `ZINC001580317763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317763 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 35, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 34, 35, 13, 13, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 896) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/896 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/896' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12) `ZINC001580317763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317763 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 40, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 39, 40, 15, 15, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317763 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 Building ZINC001580317763 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317763 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 895) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12) `ZINC001580317763.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317763 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 13, 35, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 35, 34, 35, 13, 13, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 203 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 896) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12) `ZINC001580317763.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317763.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317763 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cnn2cccnc12 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'C.2', 'C.2', 'C.2', 'N.2', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 8, 8, 1, 1, 1, 8, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 40, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 40, 39, 40, 15, 15, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317763 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317763 Building ZINC001580317834 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317834 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 897) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/897 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/897' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1) `ZINC001580317834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317834 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 23, 31, 39, 50, 50, 50, 50, 50, 9, 9, 9, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 23, 23, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 898) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/898 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/898' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1) `ZINC001580317834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317834 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 24, 31, 43, 50, 50, 50, 50, 50, 8, 8, 8, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317834 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 Building ZINC001580317834 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317834 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 897) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/897: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1) `ZINC001580317834.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317834 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 12, 12, 12, 23, 31, 39, 50, 50, 50, 50, 50, 9, 9, 9, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 23, 23, 37, 37, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 185 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 898) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/898: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1) `ZINC001580317834.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317834.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317834 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [8, 5, 8, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 11, 11, 11, 24, 31, 43, 50, 50, 50, 50, 50, 8, 8, 8, 5, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 24, 24, 41, 41, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317834 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317834 Building ZINC001580317835 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317835 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 899) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/899 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/899' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1) `ZINC001580317835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317835 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 27, 33, 38, 50, 50, 50, 50, 50, 14, 14, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 900) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/900 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/900' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1) `ZINC001580317835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317835 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 22, 33, 39, 50, 50, 50, 50, 50, 10, 10, 10, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 22, 22, 39, 39, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317835 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 Building ZINC001580317835 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317835 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 899) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/899: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1) `ZINC001580317835.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317835 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 14, 18, 18, 18, 27, 33, 38, 50, 50, 50, 50, 50, 14, 14, 14, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 18, 27, 27, 38, 38, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 191 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 900) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/900: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1) `ZINC001580317835.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317835.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317835 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC[C@H]1CCOC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'O.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 7, 5, 5, 12, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [10, 6, 10, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 10, 13, 13, 13, 22, 33, 39, 50, 50, 50, 50, 50, 10, 10, 10, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 13, 22, 22, 39, 39, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317835 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317835 Building ZINC001580317952 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317952 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 901) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/901 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/901' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001580317952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317952 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 902) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/902 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/902' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001580317952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317952 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 23, 23, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317952 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 Building ZINC001580317952 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317952 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 901) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/901: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001580317952.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317952 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 22, 22, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 902) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/902: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21) `ZINC001580317952.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317952.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317952 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 7, 13, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 23, 23, 29, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 13, 13, 13, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 175 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317952 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317952 Building ZINC001580317953 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317953 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 903) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/903 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/903' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001580317953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317953 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 904) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/904 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/904' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001580317953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317953 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 26, 26, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317953 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 Building ZINC001580317953 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317953 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 903) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001580317953.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317953 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 904) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21) `ZINC001580317953.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317953.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580317953 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CCCc2nn[nH]c21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.2', 'N.pl3', 'H', '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, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 5, 1, 8, 8, 8, 6, 1, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 17, 26, 26, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 10, 10, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [43, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 44, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 45, 46, 47, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317953 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317953 Building ZINC001580317971 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317971 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 905) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/905 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/905' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1) `ZINC001580317971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317971 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 19, 19, 19, 34, 48, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 906) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/906 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/906' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1) `ZINC001580317971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317971 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 19, 34, 49, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317971 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 Building ZINC001580317971 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580317971 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 905) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1) `ZINC001580317971.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580317971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317971 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 12, 19, 19, 19, 34, 48, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 7, 7, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 906) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1) `ZINC001580317971.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580317971.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580317971 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)COC1CCOCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 12, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 3, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 12, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 19, 19, 19, 34, 49, 50, 50, 50, 50, 50, 12, 12, 12, 7, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 19, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 168 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580317971 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580317971 Building ZINC001580318003 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318003 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 907) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/907 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/907' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001580318003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580318003 none Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 30, 16, 30, 30, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 49, 30, 30, 30, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 908) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/908 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/908' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001580318003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580318003 none Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 34, 19, 34, 34, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 34, 34, 34, 19, 19, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318003 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 Building ZINC001580318003 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318003 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 907) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001580318003.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580318003 none Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 49, 49, 49, 30, 16, 30, 30, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 49, 30, 30, 30, 17, 17, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 209 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 908) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1) `ZINC001580318003.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318003.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580318003 none Cc1cc(=O)c(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c[nH]1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 6, 7, 7, 7, 7, 6, 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, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 47, 47, 47, 34, 19, 34, 34, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 47, 34, 34, 34, 19, 19, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48]) total number of confs: 205 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318003 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318003 Building ZINC001580318023 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318023 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 909) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/909 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/909' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1) `ZINC001580318023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318023 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 42, 50, 50, 50, 50, 50, 50, 9, 9, 9, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 910) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/910 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/910' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1) `ZINC001580318023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318023 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 48, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318023 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 Building ZINC001580318023 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318023 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 909) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1) `ZINC001580318023.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318023 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 42, 50, 50, 50, 50, 50, 50, 9, 9, 9, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 29, 29, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 162 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 910) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1) `ZINC001580318023.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318023.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318023 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 15, 15, 15, 48, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 15, 36, 36, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318023 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318023 Building ZINC001580318025 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318025 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 911) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/911 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/911' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1) `ZINC001580318025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318025 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 38, 50, 50, 50, 50, 50, 50, 9, 9, 9, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 912) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/912 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/912' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1) `ZINC001580318025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318025 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318025 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 Building ZINC001580318025 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318025 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 911) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/911: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1) `ZINC001580318025.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318025 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 9, 10, 10, 10, 38, 50, 50, 50, 50, 50, 50, 9, 9, 9, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 10, 28, 28, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 173 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 912) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/912: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1) `ZINC001580318025.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318025.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318025 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C[C@@H]1COC(=O)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'H', 'C.3', 'O.3', 'C.2', 'O.2', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 5, 7, 5, 12, 1, 11, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 3, 7, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [13, 9, 13, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 13, 16, 16, 16, 44, 50, 50, 50, 50, 50, 50, 13, 13, 13, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 39, 39, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318025 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318025 Building ZINC001580318136 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318136 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 913) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/913 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/913' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O) `ZINC001580318136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318136 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 24, 45, 50, 50, 50, 50, 50, 50, 19, 19, 19, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 914) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/914 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/914' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O) `ZINC001580318136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318136 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 18, 18, 18, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318136 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 Building ZINC001580318136 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318136 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 913) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/913: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O) `ZINC001580318136.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318136 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [19, 12, 19, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 19, 24, 24, 24, 45, 50, 50, 50, 50, 50, 50, 19, 19, 19, 12, 12, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 45, 45, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 200 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 914) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/914: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O) `ZINC001580318136.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318136.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318136 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)Cn1ccccc1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 1, 1, 1, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [18, 11, 18, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 25, 25, 25, 46, 50, 50, 50, 50, 50, 50, 18, 18, 18, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 25, 46, 46, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318136 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318136 Building ZINC001580318160 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318160 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 915) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/915 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/915' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001580318160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580318160 none Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 23, 23, 23, 19, 13, 19, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 23, 19, 19, 19, 13, 13, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 916) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/916 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/916' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001580318160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580318160 none Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 26, 26, 26, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 18, 18, 18, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318160 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 Building ZINC001580318160 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318160 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 915) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001580318160.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580318160 none Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 45, 23, 23, 23, 19, 13, 19, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 45, 45, 23, 19, 19, 19, 13, 13, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 207 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 916) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O) `ZINC001580318160.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318160.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580318160 none Cc1cccn(CC(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 1, 8, 5, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 46, 26, 26, 26, 18, 12, 18, 18, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 46, 46, 26, 18, 18, 18, 12, 12, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 50, 51, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42]) total number of confs: 202 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318160 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318160 Building ZINC001580318161 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318161 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 917) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/917 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/917' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21) `ZINC001580318161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318161 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 918) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/918 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/918' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21) `ZINC001580318161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318161 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 36, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318161 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 Building ZINC001580318161 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318161 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 917) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/917: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21) `ZINC001580318161.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318161 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 16, 36, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 918) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/918: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21) `ZINC001580318161.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318161.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318161 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccc2ncnn21 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'C.2', 'N.2', 'N.pl3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 1, 8, 1, 8, 8, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 15, 36, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 50, 36, 36, 36, 16, 16, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318161 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318161 Building ZINC001580318173 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318173 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 919) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/919 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/919' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1) `ZINC001580318173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318173 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 40, 40, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 920) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/920 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/920' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1) `ZINC001580318173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318173 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 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: [33, 16, 33, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 42, 42, 42, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318173 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 Building ZINC001580318173 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318173 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 919) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/919: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1) `ZINC001580318173.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318173 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 17, 31, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 40, 40, 40, 50, 50, 50, 50, 50, 50, 31, 31, 31, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 40, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 920) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/920: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1) `ZINC001580318173.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318173.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318173 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cc(=O)n(C)o1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', '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'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 11, 8, 5, 12, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 6, 7, 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: [33, 16, 33, 13, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 42, 42, 42, 50, 50, 50, 50, 50, 50, 33, 33, 33, 16, 16, 13, 13, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 42, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45]) total number of confs: 189 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318173 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318173 Building ZINC001580318356 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318356 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 921) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/921 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/921' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1) `ZINC001580318356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318356 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 22, 22, 22, 36, 46, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 922) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/922 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/922' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1) `ZINC001580318356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318356 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 22, 22, 22, 32, 48, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318356 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 Building ZINC001580318356 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318356 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 921) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/921: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1) `ZINC001580318356.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318356 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 22, 22, 22, 36, 46, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 158 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 922) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/922: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1) `ZINC001580318356.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318356.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318356 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 22, 22, 22, 32, 48, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318356 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318356 Building ZINC001580318357 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318357 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 923) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/923 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/923' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1) `ZINC001580318357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318357 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 23, 23, 23, 36, 48, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 924) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/924 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/924' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1) `ZINC001580318357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318357 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 24, 24, 24, 33, 49, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318357 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 Building ZINC001580318357 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318357 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 923) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/923: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1) `ZINC001580318357.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318357 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 23, 23, 23, 36, 48, 50, 50, 50, 50, 50, 50, 14, 14, 14, 6, 6, 6, 6, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 23, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 40, 41, 36, 38, 42, 39, 37] set([0, 1, 2, 3, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 924) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/924: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1) `ZINC001580318357.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318357.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318357 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)C(=O)N1CC[C@@H](C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 7, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 15, 24, 24, 24, 33, 49, 50, 50, 50, 50, 50, 50, 15, 15, 15, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38, 42] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 153 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318357 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318357 Building ZINC001580318362 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318362 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 925) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/925 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/925' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001580318362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580318362 none COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 15, 34, 34, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 926) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/926 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/926' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001580318362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580318362 none COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 16, 34, 34, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 16, 16, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318362 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 Building ZINC001580318362 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318362 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 925) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001580318362.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580318362 none COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 15, 34, 34, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 15, 15, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 206 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 926) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1) `ZINC001580318362.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318362.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 16 0 4 16 1 4 16 2 3 16 2 19 to be deleted 20 to be deleted 21 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580318362 none COc1cc(C(=O)N[C@H](C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)ncn1 NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.ar', 'C.ar', 'N.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 1, 11, 8, 5, 7, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 8, 7, 7, 7, 7, 6, 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, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 3, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 34, 16, 34, 34, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 34, 34, 34, 16, 16, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50] 50 rigid atoms, others: [38, 39, 40, 41, 42, 43, 44, 45, 14, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 47]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318362 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318362 Building ZINC001580318368 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318368 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 927) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/927 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/927' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O) `ZINC001580318368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580318368 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 32, 32, 32, 47, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 928) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/928 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/928' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O) `ZINC001580318368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580318368 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 11, 25, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 31, 31, 31, 49, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 49, 49, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318368 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 Building ZINC001580318368 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318368 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 927) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/927: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O) `ZINC001580318368.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580318368 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [23, 11, 23, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 23, 32, 32, 32, 47, 50, 50, 50, 50, 50, 23, 23, 23, 11, 11, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 32, 47, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 204 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 928) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/928: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O) `ZINC001580318368.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318368.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 53 natoms 52 natoms 51 natoms 50 names: ZINC001580318368 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CN1CCCC1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 5, 5, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [25, 11, 25, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 31, 31, 31, 49, 50, 50, 50, 50, 50, 25, 25, 25, 11, 11, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 31, 49, 49, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 41, 42, 43, 44, 45, 46, 47, 48, 49]) total number of confs: 209 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318368 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318368 Building ZINC001580318531 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318531 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 929) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/929 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/929' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O) `ZINC001580318531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318531 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 930) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/930 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/930' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O) `ZINC001580318531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318531 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 15, 32, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318531 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 Building ZINC001580318531 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318531 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 929) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O) `ZINC001580318531.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318531 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 17, 33, 12, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 33, 46, 46, 46, 50, 50, 50, 50, 50, 50, 50, 33, 33, 33, 17, 17, 12, 12, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 46, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 930) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O) `ZINC001580318531.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318531.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 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: ZINC001580318531 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)c1cccn(C)c1=O NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [32, 15, 32, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 32, 47, 47, 47, 50, 50, 50, 50, 50, 50, 50, 32, 32, 32, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 47, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 201 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318531 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318531 Building ZINC001580318550 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580318550 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 931) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/931 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/931' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 932) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/932 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/932' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 933) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/933 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/933' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 934) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/934 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/934' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318550 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 Building ZINC001580318550 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580318550 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 931) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 932) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 933) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 934) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318550 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 Building ZINC001580318550 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580318550 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 931) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 932) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 933) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 934) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318550 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 Building ZINC001580318550 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580318550 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 931) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/931: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 932) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/932: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1) `ZINC001580318550.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 933) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/933: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 18, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 24, 24, 28, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 12, 12, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 24, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 934) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/934: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1) `ZINC001580318550.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580318550.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580318550 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)[C@H]1CC[N@@](C)CC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'H', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 7, 5, 5, 10, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 18, 26, 26, 31, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 9, 9, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53]) total number of confs: 174 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318550 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318550 Building ZINC001580318661 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318661 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 935) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/935 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/935' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1) `ZINC001580318661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318661 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 27, 32, 32, 34, 50, 50, 50, 11, 11, 11, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 27, 27, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 936) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/936 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/936' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1) `ZINC001580318661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318661 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 34, 34, 36, 50, 50, 50, 7, 7, 7, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318661 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 Building ZINC001580318661 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580318661 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 935) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/935: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1) `ZINC001580318661.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580318661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318661 none C[C@H](CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 11, 14, 14, 14, 27, 32, 32, 34, 50, 50, 50, 11, 11, 11, 8, 8, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 14, 27, 27, 32, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 936) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/936: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1) `ZINC001580318661.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580318661.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580318661 none C[C@H](CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)NC(=O)CNC(=O)C1CCC1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 1, 11, 5, 8, 1, 11, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 4, 7, 6, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 11, 11, 11, 23, 34, 34, 36, 50, 50, 50, 7, 7, 7, 6, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 11, 23, 23, 34, 50, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 37, 6, 39, 8, 9, 10, 11, 12, 13, 40, 41, 38] set([0, 1, 2, 3, 4, 5, 7, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52]) total number of confs: 195 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580318661 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580318661 Building ZINC001580349761 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580349761 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 937) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/937 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/937' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580349761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580349761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580349761 none C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 30, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 29, 30, 48, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 938) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/938 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/938' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580349761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580349761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580349761 none C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 18, 30, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 30, 29, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580349761 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 Building ZINC001580349761 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580349761 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 937) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/937: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580349761.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580349761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580349761 none C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 19, 30, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 20, 20, 29, 30, 48, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 208 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 938) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/938: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580349761.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580349761.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580349761 none C[C@H](CCNC(=O)c1cnc2cccnn21)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 8, 1, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 18, 30, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 19, 19, 30, 29, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 214 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580349761 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580349761 Building ZINC001580370479 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580370479 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 939) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/939 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/939' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580370479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580370479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580370479 none C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 26, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 26, 25, 43, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 940) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/940 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/940' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580370479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580370479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580370479 none C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 24, 23, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580370479 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 Building ZINC001580370479 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580370479 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 939) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/939: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580370479.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580370479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580370479 none C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 17, 26, 43, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 18, 18, 26, 25, 43, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 940) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/940: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580370479.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580370479.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580370479 none C[C@H](CCNC(=O)c1ccnc2ccnn21)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.2', 'C.2', 'C.2', 'C.2', 'N.2', 'N.pl3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 1, 1, 1, 8, 8, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 24, 49, 49, 49, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 24, 23, 49, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 18, 20, 21, 22, 23, 24, 25] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 197 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580370479 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580370479 Building ZINC001580375559 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580375559 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 941) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/941 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/941' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001580375559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580375559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580375559 none Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 41, 22, 15, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 21, 22, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 942) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/942 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/942' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001580375559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580375559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580375559 none Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 48, 48, 24, 14, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 48, 24, 23, 15, 15, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580375559 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 Building ZINC001580375559 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580375559 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 941) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001580375559.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580375559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580375559 none Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 41, 41, 41, 22, 15, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 21, 22, 16, 16, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 942) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C) `ZINC001580375559.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580375559.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 55 natoms 54 natoms 53 natoms 52 names: ZINC001580375559 none Cc1cc(=O)c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cn1C NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'O.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 11, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 5, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 3, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 48, 48, 48, 24, 14, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 48, 24, 23, 15, 15, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 15, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 48, 49, 50, 51]) total number of confs: 192 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580375559 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580375559 Building ZINC001580379317 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580379317 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 943) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/943 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/943' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580379317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580379317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580379317 none C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 20, 31, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 31, 30, 48, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 944) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/944 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/944' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580379317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580379317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580379317 none C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 16, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 25, 26, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580379317 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 Building ZINC001580379317 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580379317 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 943) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580379317.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580379317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580379317 none C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 20, 31, 48, 48, 48, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 21, 21, 31, 30, 48, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 944) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580379317.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580379317.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 51 natoms 50 natoms 49 natoms 48 names: ZINC001580379317 none C[C@H](CCNC(=O)c1cc2n(n1)CCO2)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.pl3', 'N.2', 'C.3', 'C.3', 'O.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 8, 5, 5, 12, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 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] 0 hydrogens 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, 7, 16, 26, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 17, 17, 25, 26, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [39, 40, 41, 42, 43, 44, 45, 46, 47, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38]) total number of confs: 199 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580379317 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580379317 Building ZINC001580393695 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580393695 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 945) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/945 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/945' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580393695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580393695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580393695 none C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 18, 18, 22, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 946) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/946 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/946' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580393695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580393695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580393695 none C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 18, 22, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 22, 22, 25, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580393695 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 Building ZINC001580393695 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580393695 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 945) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580393695.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580393695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580393695 none C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 15, 18, 22, 22, 22, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 15, 15, 18, 18, 22, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 141 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 946) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580393695.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580393695.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580393695 none C[C@H](CCNC(=O)c1ccn(C)c(=O)c1)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'C.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 8, 5, 1, 11, 1, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 8, 8, 18, 22, 25, 25, 25, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 8, 8, 8, 18, 18, 22, 22, 25, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 147 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580393695 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393695 Building ZINC001580393751 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580393751 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 947) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/947 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/947' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580393751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580393751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393751 none C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 13, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 13, 13, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 948) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/948 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/948' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580393751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580393751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393751 none C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 11, 19, 19, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 11, 11, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580393751 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 Building ZINC001580393751 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580393751 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 947) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580393751.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580393751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393751 none C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 10, 13, 22, 22, 31, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 10, 10, 13, 13, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 170 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 948) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580393751.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580393751.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393751 none C[C@H](CCNC(=O)[C@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 11, 19, 19, 25, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 11, 11, 19, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 166 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580393751 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393751 Building ZINC001580393752 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580393752 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 949) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/949 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/949' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580393752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580393752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393752 none C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 16, 22, 22, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 16, 16, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 950) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/950 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/950' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580393752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580393752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393752 none C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 14, 20, 20, 26, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 14, 14, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580393752 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 Building ZINC001580393752 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580393752 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 949) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580393752.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580393752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393752 none C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 16, 22, 22, 28, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 12, 12, 16, 16, 22, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 950) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580393752.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580393752.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 20 is the cov attach 4 20 0 4 20 1 4 20 2 3 20 2 23 to be deleted 24 to be deleted 25 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580393752 none C[C@H](CCNC(=O)[C@@H]1CCN(C)C(=O)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'H', 'C.3', 'C.3', 'N.am', 'C.3', 'C.2', 'O.2', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 7, 5, 5, 8, 5, 1, 11, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 9, 14, 20, 20, 26, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 9, 9, 14, 14, 20, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 44, 45, 46, 47, 48, 49, 18, 51, 20, 21, 22, 23, 24, 25, 52] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580393752 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580393752 Building ZINC001580412457 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580412457 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 951) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/951 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/951' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580412457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580412457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580412457 none C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 24, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 24, 23, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 952) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/952 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/952' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580412457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580412457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580412457 none C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 20, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 20, 19, 45, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580412457 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 Building ZINC001580412457 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580412457 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 951) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580412457.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580412457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580412457 none C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 7, 15, 24, 41, 41, 41, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 7, 7, 7, 16, 16, 24, 23, 41, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 180 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 952) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580412457.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580412457.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 52 natoms 51 natoms 50 natoms 49 names: ZINC001580412457 none C[C@H](CCNC(=O)c1cccn(C)c1=O)NC(=O)[C@]([O-])([SiH3])C(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.2', 'C.2', 'C.2', 'C.2', 'N.am', 'C.3', 'C.2', 'O.2', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 1, 1, 1, 1, 8, 5, 1, 11, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [5, 2, 5, 5, 12, 20, 45, 45, 45, 50, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 5, 5, 5, 13, 13, 20, 19, 45, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [40, 41, 42, 43, 44, 45, 46, 47, 48, 17, 19, 20, 21, 22, 23, 24] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 184 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580412457 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580412457 Building ZINC001580416643 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580416643 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 953) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/953 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/953' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001580416643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580416643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580416643 none COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 41, 41, 26, 17, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 25, 26, 18, 18, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 954) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/954 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/954' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001580416643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580416643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580416643 none COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 40, 22, 15, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 22, 22, 15, 15, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580416643 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 Building ZINC001580416643 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580416643 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 953) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001580416643.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580416643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580416643 none COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 41, 41, 41, 26, 17, 7, 2, 7, 7, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 41, 25, 26, 18, 18, 7, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 184 number of broken/clashed sets: 2 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 954) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C) `ZINC001580416643.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580416643.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 15 is the cov attach 4 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: ZINC001580416643 none COc1c(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)cnn1C NO_LONG_NAME dock atom types: ['C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'N.2', 'N.pl3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 12, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 8, 8, 5, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 3, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 40, 40, 40, 22, 15, 6, 2, 6, 6, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 40, 22, 22, 15, 15, 6, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [45, 37, 38, 39, 40, 41, 42, 43, 44, 13, 15, 16, 17, 18, 19, 20] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 46, 47, 48, 49]) total number of confs: 182 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580416643 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580416643 Building ZINC001580450516 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580450516 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 955) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/955 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/955' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001580450516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580450516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580450516 none CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 27, 27, 27, 16, 9, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 27, 16, 15, 10, 10, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 956) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/956 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/956' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001580450516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580450516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580450516 none CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 29, 29, 29, 13, 9, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 50, 50, 30, 29, 13, 13, 9, 9, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580450516 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 Building ZINC001580450516 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580450516 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 955) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001580450516.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580450516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580450516 none CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 31, 31, 31, 27, 27, 27, 16, 9, 4, 2, 4, 4, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 31, 50, 50, 50, 50, 50, 50, 50, 31, 27, 16, 15, 10, 10, 4, 4, 4, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 956) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1) `ZINC001580450516.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580450516.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 17 0 4 17 1 4 17 2 3 17 2 20 to be deleted 21 to be deleted 22 to be deleted natoms 54 natoms 53 natoms 52 natoms 51 names: ZINC001580450516 none CCCn1cc(C(=O)NCC[C@@H](C)NC(=O)[C@]([O-])([SiH3])C(C)(C)C)nn1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'C.3', 'N.pl3', 'C.2', 'C.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'N.2', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 5, 8, 1, 1, 1, 11, 8, 5, 5, 5, 7, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 8, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 6, 4, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 30, 30, 30, 29, 29, 29, 13, 9, 5, 2, 5, 5, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 30, 50, 50, 50, 50, 50, 50, 50, 30, 29, 13, 13, 9, 9, 5, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [50, 49, 42, 43, 44, 45, 46, 15, 48, 17, 18, 19, 20, 21, 22, 47] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 16, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41]) total number of confs: 233 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580450516 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580450516 Building ZINC001580467451 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467451 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 957) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/957 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/957' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 958) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/958 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/958' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 959) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/959 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/959' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 960) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/960 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/960' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467451 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 Building ZINC001580467451 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467451 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 957) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 958) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 959) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 960) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467451 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 Building ZINC001580467451 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467451 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 957) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 958) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 959) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 960) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467451 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 Building ZINC001580467451 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467451 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 957) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/957: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 958) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/958: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 7, 11, 11, 11, 30, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 7, 7, 11, 30, 30, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 157 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 959) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/959: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 960) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/960: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467451.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467451.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467451 none C[C@H](CCNC(=O)CN1CC[C@@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 34, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 34, 34, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 188 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467451 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467451 Building ZINC001580467452 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467452 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 961) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/961 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/961' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 962) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/962 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/962' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 963) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/963 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/963' -> `2.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 964) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/964 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/964' -> `3.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467452 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 Building ZINC001580467452 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467452 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 961) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 962) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 963) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 964) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467452 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 Building ZINC001580467452 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467452 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 961) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 962) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 963) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 964) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467452 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 Building ZINC001580467452 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 4 protomers extracted for ZINC001580467452 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 961) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 962) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 4, 8, 11, 11, 11, 32, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 4, 4, 8, 8, 11, 32, 32, 50, 50, 50, 50, 50, 50, 50, 50, 50, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [1, 50, 49, 51, 48, 44, 45, 46, 47, 16, 17, 18, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43]) total number of confs: 169 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `2' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 2 (index: 963) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/963: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 2 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `2.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `2.mol2' -> `2.mol2.original' `output.mol2' -> `2.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `3' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 3 (index: 964) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/964: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 3 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(C)(C)C) `ZINC001580467452.mol2' -> `3.mol2' `temp.mol2' -> `ZINC001580467452.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `3.mol2' -> `3.mol2.original' `output.mol2' -> `3.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 19 is the cov attach 4 19 0 4 19 1 4 19 2 3 19 2 22 to be deleted 23 to be deleted 24 to be deleted natoms 57 natoms 56 natoms 55 natoms 54 names: ZINC001580467452 none C[C@H](CCNC(=O)CN1CC[C@H](C)C1)NC(=O)[C@]([O-])([SiH3])C(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', 'N.3', 'C.3', 'C.3', 'C.3', 'H', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 8, 1, 11, 5, 10, 5, 5, 5, 7, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 4, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 2, 4, 4, 7, 11, 15, 15, 15, 35, 50, 50, 50, 50, 50, 50, 2, 1, 2, 1, 1, 1, 1, 1, 1, 4, 4, 4, 7, 7, 11, 11, 15, 35, 35, 50, 50, 50, 50, 50, 50, 50, 50, 50, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [51, 49, 45, 46, 47, 48, 17, 50, 19, 20, 21, 22, 23, 24, 52, 53] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 18, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 187 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580467452 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/1.* 2: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/2.* 3: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/3.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580467452 Building ZINC001580473692 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580473692 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 965) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/965 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/965' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001580473692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580473692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001580473692 none O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [25, 3, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 10, 5, 5] 72 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 966) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/966 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/966' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001580473692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580473692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001580473692 none O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [22, 2, 27, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 8, 4, 4] 70 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580473692 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 Building ZINC001580473692 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580473692 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 965) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001580473692.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580473692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001580473692 none O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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 72 conformations in input total number of sets (complete confs): 72 using faster count positions algorithm for large data unique positions, atoms: [25, 3, 31, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 1, 1, 1, 5, 5, 1, 1, 5, 5, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 35, 5, 5, 10, 5, 5] 72 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 89 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 966) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@@]([O-])([SiH3])c1ccc(O)cc1) `ZINC001580473692.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580473692.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 17 is the cov attach 4 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: ZINC001580473692 none O=C(N1CCc2nc[nH]c2C12CCNCC2)[C@@]([O-])([SiH3])c1ccc(O)cc1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.2', 'N.2', 'C.2', 'N.pl3', 'H', 'C.2', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'O.3', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 1, 8, 1, 8, 6, 1, 5, 5, 5, 10, 5, 5, 5, 12, 1, 1, 1, 1, 12, 1, 1, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 6, 7, 7] dock color type numbers: [6, 9, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 7, 7, 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 70 conformations in input total number of sets (complete confs): 70 using faster count positions algorithm for large data unique positions, atoms: [22, 2, 27, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 1, 1, 1, 4, 4, 1, 1, 4, 4, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 31, 4, 4, 8, 4, 4] 70 rigid atoms, others: [17, 18, 19] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44]) total number of confs: 76 number of broken/clashed sets: 6 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580473692 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580473692 Building ZINC001580616176 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580616176 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 967) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/967 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/967' -> `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)Nc1cc(c2nn[nH]n2)cc(C)n1) `ZINC001580616176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580616176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001580616176 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2nn[nH]n2)cc(C)n1 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.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', '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, 8, 8, 8, 6, 8, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 17, 17, 17, 17, 17] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 968) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/968 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/968' -> `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)Nc1cc(c2nn[nH]n2)cc(C)n1) `ZINC001580616176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580616176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001580616176 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2nn[nH]n2)cc(C)n1 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.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', '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, 8, 8, 8, 6, 8, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 16, 16, 16, 16, 16] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580616176 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 Building ZINC001580616176 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580616176 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 967) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2nn[nH]n2)cc(C)n1) `ZINC001580616176.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580616176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001580616176 none Cc1nn(C)c(C)c1[C@]([O-])([SiH3])C(=O)Nc1cc(c2nn[nH]n2)cc(C)n1 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.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', '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, 8, 8, 8, 6, 8, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 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, 6, 6, 6, 1, 1, 1, 1, 10, 10, 10, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 17, 6, 6, 6, 6, 6, 6, 6, 6, 6, 10, 17, 17, 17, 17, 17] 29 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 40 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 968) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2nn[nH]n2)cc(C)n1) `ZINC001580616176.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580616176.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 8 is the cov attach 4 8 0 4 8 1 4 8 2 3 8 2 11 to be deleted 12 to be deleted 13 to be deleted natoms 44 natoms 43 natoms 42 natoms 41 names: ZINC001580616176 none Cc1nn(C)c(C)c1[C@@]([O-])([SiH3])C(=O)Nc1cc(c2nn[nH]n2)cc(C)n1 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.2', 'N.2', 'N.2', 'N.pl3', 'H', 'N.2', 'C.ar', 'C.ar', 'C.3', 'N.ar', '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, 8, 8, 8, 6, 8, 1, 1, 5, 8, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 9, 8, 10, 11, 6, 4, 7, 7, 7, 7, 7, 7, 4, 7, 7, 7, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 23 conformations in input total number of sets (complete confs): 23 using default count positions algorithm for smaller data unique positions, atoms: [5, 5, 5, 5, 5, 5, 5, 1, 1, 1, 1, 10, 10, 10, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 5, 5, 5, 5, 5, 5, 5, 5, 5, 10, 16, 16, 16, 16, 16] 23 rigid atoms, others: [8, 9, 10, 7] set([0, 1, 2, 3, 4, 5, 6, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40]) total number of confs: 37 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580616176 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580616176 Building ZINC001580667096 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580667096 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 969) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/969 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/969' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580667096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667096 none O=C(NC[C@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 20, 30, 30, 30, 30, 30, 30, 1, 1, 1, 8, 8, 8, 8, 8, 2, 14, 14, 30, 30, 30, 30, 30, 30, 30, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 970) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/970 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/970' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580667096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667096 none O=C(NC[C@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 35, 35, 35, 35, 35, 35, 1, 1, 1, 9, 9, 9, 9, 9, 4, 19, 19, 35, 35, 35, 35, 35, 35, 35, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580667096 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 Building ZINC001580667096 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580667096 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 969) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/969: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667096.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580667096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667096 none O=C(NC[C@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [2, 1, 2, 2, 20, 30, 30, 30, 30, 30, 30, 1, 1, 1, 8, 8, 8, 8, 8, 2, 14, 14, 30, 30, 30, 30, 30, 30, 30, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 99 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 970) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/970: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667096.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580667096.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667096 none O=C(NC[C@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 25, 35, 35, 35, 35, 35, 35, 1, 1, 1, 9, 9, 9, 9, 9, 4, 19, 19, 35, 35, 35, 35, 35, 35, 35, 9, 9] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 114 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580667096 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667096 Building ZINC001580667097 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580667097 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 971) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/971 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/971' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580667097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667097 none O=C(NC[C@@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 32, 32, 32, 32, 1, 1, 1, 8, 8, 8, 8, 8, 3, 17, 17, 32, 32, 32, 32, 32, 32, 32, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 972) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/972 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/972' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580667097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667097 none O=C(NC[C@@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 8, 4, 17, 17, 36, 36, 36, 36, 36, 36, 36, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580667097 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 Building ZINC001580667097 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580667097 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 971) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/971: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667097.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580667097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667097 none O=C(NC[C@@H]1CNCCO1)[C@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need 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, 32, 32, 32, 32, 32, 32, 1, 1, 1, 8, 8, 8, 8, 8, 3, 17, 17, 32, 32, 32, 32, 32, 32, 32, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 110 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 972) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/972: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NC[C@@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1) `ZINC001580667097.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580667097.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 11 is the cov attach 4 11 0 4 11 1 4 11 2 3 11 2 14 to be deleted 15 to be deleted 16 to be deleted natoms 34 natoms 33 natoms 32 natoms 31 names: ZINC001580667097 none O=C(NC[C@@H]1CNCCO1)[C@@]([O-])([SiH3])c1ccc(Br)s1 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'H', 'C.3', 'N.3', 'C.3', 'C.3', 'O.3', 'C.3', 'O.3', 'C.2', 'C.2', 'C.2', 'C.2', 'Br', 'S.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 7, 5, 10, 5, 5, 12, 5, 12, 1, 1, 1, 1, 17, 14, 6, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 3, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [4, 1, 4, 4, 23, 36, 36, 36, 36, 36, 36, 1, 1, 1, 8, 8, 8, 8, 8, 4, 17, 17, 36, 36, 36, 36, 36, 36, 36, 8, 8] 50 rigid atoms, others: [1, 11, 12, 13] set([0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30]) total number of confs: 119 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580667097 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580667097 Building ZINC001580682875 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580682875 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 973) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/973 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/973' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580682875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580682875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001580682875 none O=C(NCCCN1CCNCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 18, 21, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 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, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 974) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/974 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/974' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580682875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580682875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001580682875 none O=C(NCCCN1CCNCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 18, 21, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 21, 21, 21, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 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, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580682875 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 Building ZINC001580682875 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580682875 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 973) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/973: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580682875.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580682875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001580682875 none O=C(NCCCN1CCNCC1)[C@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 18, 21, 34, 34, 34, 34, 34, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 21, 21, 21, 21, 34, 34, 34, 34, 34, 34, 34, 34, 34, 4, 4, 4, 4] 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, 44]) total number of confs: 130 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 974) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/974: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: O=C(NCCCN1CCNCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21) `ZINC001580682875.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580682875.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 12 is the cov attach 4 12 0 4 12 1 4 12 2 3 12 2 15 to be deleted 16 to be deleted 17 to be deleted natoms 48 natoms 47 natoms 46 natoms 45 names: ZINC001580682875 none O=C(NCCCN1CCNCC1)[C@@]([O-])([SiH3])c1c[nH]c2cc(F)ccc21 NO_LONG_NAME dock atom types: ['O.2', 'C.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'N.3', 'C.3', 'C.3', 'C.3', 'O.3', 'C.2', 'C.2', 'N.pl3', 'H', 'C.ar', 'C.ar', 'C.ar', 'F', 'C.ar', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [11, 1, 8, 5, 5, 5, 10, 5, 5, 10, 5, 5, 5, 12, 1, 1, 8, 6, 1, 1, 1, 15, 1, 1, 1, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [6, 9, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 8, 10, 11, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [3, 1, 3, 3, 13, 18, 21, 32, 32, 32, 32, 32, 1, 1, 1, 4, 4, 4, 4, 4, 4, 4, 4, 4, 4, 3, 13, 13, 21, 21, 21, 21, 32, 32, 32, 32, 32, 32, 32, 32, 32, 4, 4, 4, 4] 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, 44]) total number of confs: 128 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580682875 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580682875 Building ZINC001580692019 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692019 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 975) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/975 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/975' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692019 none C[C@@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 26, 33, 18, 21, 14, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 976) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/976 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/976' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692019 none C[C@@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 25, 33, 17, 21, 14, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692019 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 Building ZINC001580692019 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692019 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 975) grep: /scratch/xiaobo/167320/xcr-8058097.70/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]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692019.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692019 none C[C@@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 26, 33, 18, 21, 14, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 18, 18, 18, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 976) grep: /scratch/xiaobo/167320/xcr-8058097.70/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]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692019.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692019.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692019 none C[C@@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 25, 33, 17, 21, 14, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 146 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692019 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692019 Building ZINC001580692020 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692020 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 977) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/977 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/977' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692020 none C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 25, 34, 17, 21, 14, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 978) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/978 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/978' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692020 none C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 25, 32, 17, 20, 13, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692020 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 Building ZINC001580692020 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692020 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 977) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692020.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692020 none C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 47, 25, 34, 17, 21, 14, 17, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 148 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 978) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692020.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692020.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692020 none C[C@H]1CCCN(C(=O)C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.3', 'H', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 5, 7, 5, 5, 5, 8, 1, 11, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 46, 25, 32, 17, 20, 13, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 17, 17, 17, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 144 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692020 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692020 Building ZINC001580692069 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692069 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 979) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/979 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/979' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1) `ZINC001580692069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692069 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 15, 15, 16, 16, 15, 15, 39, 50, 50, 16, 16, 12, 12, 12, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 39, 50, 50, 16, 16] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 980) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/980 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/980' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1) `ZINC001580692069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692069 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 15, 15, 16, 16, 15, 15, 39, 50, 50, 16, 16, 12, 12, 12, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 39, 50, 50, 16, 16] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692069 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 Building ZINC001580692069 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692069 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 979) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1) `ZINC001580692069.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692069 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 8, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 15, 15, 16, 16, 15, 15, 39, 50, 50, 16, 16, 12, 12, 12, 10, 10, 8, 8, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 39, 50, 50, 16, 16] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47, 48]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 980) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1) `ZINC001580692069.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692069.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692069 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc(NC(N)=O)cc1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.am', 'C.2', 'N.am', 'O.2', 'C.ar', 'C.ar', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 8, 1, 8, 11, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 6, 6, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 7, 4, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [12, 10, 7, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 12, 15, 15, 16, 16, 15, 15, 39, 50, 50, 16, 16, 12, 12, 12, 10, 10, 7, 7, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 16, 16, 39, 50, 50, 16, 16] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 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/167320/xcr-8058097.70/working/building/ZINC001580692069 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692069 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692069 Building ZINC001580692309 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692309 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 981) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/981 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/981' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2) `ZINC001580692309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692309 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 982) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/982 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/982' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2) `ZINC001580692309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692309 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692309 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 Building ZINC001580692309 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692309 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 981) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2) `ZINC001580692309.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692309 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [27, 17, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 27, 43, 43, 50, 50, 50, 50, 50, 50, 50, 50, 50, 27, 27, 27, 17, 17, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 167 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 982) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2) `ZINC001580692309.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692309.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692309 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1ccc2c(n1)OCCO2 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.ar', 'O.3', 'C.3', 'C.3', 'O.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 12, 5, 5, 12, 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, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 3, 3, 7, 7, 3, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [28, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 28, 44, 44, 50, 50, 50, 50, 50, 50, 50, 50, 50, 28, 28, 28, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 171 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692309 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692309 Building ZINC001580692314 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692314 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 983) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/983 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/983' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692314 none CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 22, 30, 15, 22, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 984) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/984 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/984' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692314 none CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 28, 50, 16, 26, 14, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692314 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 Building ZINC001580692314 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692314 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 983) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/983: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692314.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692314 none CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 50, 50, 50, 50, 31, 50, 22, 30, 15, 22, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 22, 22, 22, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 181 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 984) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/984: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692314.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692314.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692314 none CC(=O)N1CCC[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 28, 50, 16, 26, 14, 16, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 16, 16, 16, 14, 14, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 173 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692314 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692314 Building ZINC001580692315 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692315 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 985) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/985 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/985' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692315 none CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 30, 49, 15, 22, 13, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 49, 49, 49, 49, 49, 49, 15, 15, 15, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 166 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 986) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/986 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/986' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692315 none CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 23, 31, 15, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692315 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 Building ZINC001580692315 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692315 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 985) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/985: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 0 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692315.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692315 none CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 49, 50, 49, 49, 49, 49, 30, 49, 15, 22, 13, 15, 9, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 49, 50, 50, 50, 49, 49, 49, 49, 49, 49, 15, 15, 15, 13, 13, 9, 9, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 49, 49] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 166 number of broken/clashed sets: 7 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 986) grep: /scratch/xiaobo/167320/xcr-8058097.70/working/3D/986: No such file or directory No valid previously generated conformations found! Embedding SMILES in 3D and adding Hydrogens for 1 We are using corina for 3D embeding debuging info:: - /nfs/soft/corina/current/corina -i t=smiles -o t=mol2 -d rc,flapn,de=6,mc=1,wh removed `corina.trc' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1) `ZINC001580692315.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692315.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580692315 none CC(=O)N1CCC[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 11, 8, 5, 5, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 23, 31, 15, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [48, 50, 42, 43, 44, 45, 46, 47, 16, 49, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 51, 52]) total number of confs: 180 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692315 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692315 Building ZINC001580692342 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692342 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 987) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/987 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/987' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl) `ZINC001580692342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692342 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 44, 44, 50, 50, 50, 50, 50, 50, 35, 35, 35, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 988) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/988 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/988' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl) `ZINC001580692342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692342 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 45, 45, 50, 50, 50, 50, 50, 50, 36, 36, 36, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692342 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 Building ZINC001580692342 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692342 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 987) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl) `ZINC001580692342.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692342 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 35, 44, 44, 50, 50, 50, 50, 50, 50, 35, 35, 35, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 988) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl) `ZINC001580692342.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692342.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692342 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cn(C)nc1Cl NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'N.2', 'C.2', 'Cl', 'H', 'H', 'H', '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, 5, 5, 5, 5, 1, 11, 1, 1, 8, 5, 8, 1, 16, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 22, 14, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 36, 45, 45, 50, 50, 50, 50, 50, 50, 36, 36, 36, 22, 22, 14, 14, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [32, 33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 37, 30, 31] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 39, 40, 41, 42]) total number of confs: 179 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692342 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692342 Building ZINC001580692366 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692366 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 989) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/989 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/989' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21) `ZINC001580692366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692366 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 990) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/990 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/990' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21) `ZINC001580692366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692366 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692366 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 Building ZINC001580692366 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692366 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 989) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21) `ZINC001580692366.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692366 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [30, 18, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 30, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 30, 30, 30, 18, 18, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 176 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 990) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21) `ZINC001580692366.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692366.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692366 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cccc2nnn(C)c21 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'N.2', 'N.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', 'H', 'H'] dock atom type numbers: [5, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 1, 1, 1, 8, 8, 8, 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] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [31, 19, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 31, 42, 42, 50, 50, 50, 50, 50, 50, 50, 50, 50, 31, 31, 31, 19, 19, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43, 44, 45, 46, 47]) total number of confs: 175 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692366 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692366 Building ZINC001580692373 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692373 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 991) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/991 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/991' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(COCC(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001580692373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580692373 none Cc1cc(COCC(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 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, 3, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 29, 21, 6, 6, 6, 6, 6, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 6, 6, 6, 6, 6, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 992) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/992 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/992' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1cc(COCC(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001580692373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580692373 none Cc1cc(COCC(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 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, 3, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 30, 22, 7, 7, 7, 7, 7, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 22, 22, 7, 7, 7, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692373 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 Building ZINC001580692373 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692373 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 991) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cc(COCC(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001580692373.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580692373 none Cc1cc(COCC(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 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, 3, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 29, 21, 6, 6, 6, 6, 6, 5, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 21, 21, 6, 6, 6, 6, 6, 5, 5, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 193 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 992) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1cc(COCC(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)on1) `ZINC001580692373.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692373.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 16 is the cov attach 4 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: ZINC001580692373 none Cc1cc(COCC(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)on1 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'C.2', 'C.2', 'C.3', 'O.3', 'C.3', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'O.3', 'N.2', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 1, 1, 5, 12, 5, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 12, 8, 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, 3, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations in input total number of sets (complete confs): 50 using default count positions algorithm for smaller data unique positions, atoms: [50, 50, 50, 46, 30, 22, 7, 7, 7, 7, 7, 6, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 46, 46, 22, 22, 7, 7, 7, 7, 7, 6, 6, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 14, 47, 16, 17, 18, 19, 20, 21, 46] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 15, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 190 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692373 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692373 Building ZINC001580692701 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692701 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 993) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/993 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/993' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001580692701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001580692701 none CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations 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, 26, 23, 26, 16, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 994) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/994 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/994' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001580692701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001580692701 none CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations 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, 25, 23, 25, 16, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692701 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 Building ZINC001580692701 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692701 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 993) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001580692701.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001580692701 none CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations 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, 26, 23, 26, 16, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 138 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 994) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1) `ZINC001580692701.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692701.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.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 52 natoms 51 natoms 50 natoms 49 names: ZINC001580692701 none CNC(=O)c1cccc(C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)n1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.2', 'O.2', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.ar', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', '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, 8, 1, 11, 1, 1, 1, 1, 1, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 8, 7, 7, 7, 6, 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, 4, 7, 6, 7, 7, 7, 7, 7, 7, 6, 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] 0 hydrogens need rotated 50 conformations 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, 25, 23, 25, 16, 23, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 23, 23, 23, 16, 16, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39]) total number of confs: 135 number of broken/clashed sets: 0 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692701 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692701 Building ZINC001580692929 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692929 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 995) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/995 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/995' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1) `ZINC001580692929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692929 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', '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, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 996) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/996 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/996' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1) `ZINC001580692929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692929 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', '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, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692929 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 Building ZINC001580692929 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580692929 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 995) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1) `ZINC001580692929.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580692929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692929 none CN(CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', '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, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 25, 36, 36, 50, 50, 50, 50, 50, 50, 50, 50, 50, 25, 25, 25, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 155 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 996) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1) `ZINC001580692929.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580692929.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 7 is the cov attach 4 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: ZINC001580692929 none CN(CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)C(=O)c1cnc2[nH]nnc2c1 NO_LONG_NAME dock atom types: ['C.3', 'N.am', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.2', 'O.2', 'C.ar', 'C.ar', 'N.ar', 'C.ar', 'N.pl3', 'H', 'N.2', '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, 8, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 1, 11, 1, 1, 8, 1, 8, 6, 8, 8, 1, 1, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 6, 7, 7, 3, 7, 4, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens 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, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 26, 37, 37, 50, 50, 50, 50, 50, 50, 50, 50, 50, 26, 26, 26, 14, 14, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50] 50 rigid atoms, others: [33, 34, 35, 36, 5, 38, 7, 8, 9, 10, 11, 12, 40, 41, 39, 37] set([0, 1, 2, 3, 4, 6, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 42, 43]) total number of confs: 156 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580692929 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580692929 Building ZINC001580693000 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580693000 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 997) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/997 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/997' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580693000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693000 none Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 20, 29, 13, 20, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 998) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/998 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/998' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580693000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693000 none Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 50, 20, 29, 15, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580693000 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 Building ZINC001580693000 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580693000 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 997) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693000.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580693000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693000 none Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 20, 29, 13, 20, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 4 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 998) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693000.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580693000.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693000 none Cc1ncc2n1C[C@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 50, 20, 29, 15, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 3 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580693000 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693000 Building ZINC001580693001 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580693001 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 999) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/999 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/999' -> `0.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580693001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693001 none Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 50, 20, 29, 15, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 1000) Found valid previously generated 3D confromation in /scratch/xiaobo/167320/xcr-8058097.70/working/3D/1000 `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/1000' -> `1.mol2' Preparing input files Starting the preparation of the solvation calculations (AMSOL7.1) (SMILES: Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580693001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693001 none Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 21, 29, 13, 21, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580693001 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 Building ZINC001580693001 mkdir: created directory `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Extracting previously generated protomers and correcting pH mod types 2 protomers extracted for ZINC001580693001 mkdir: created directory `0' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/0 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 0 (index: 999) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693001.mol2' -> `0.mol2' `temp.mol2' -> `ZINC001580693001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/0/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `0.mol2' -> `0.mol2.original' `output.mol2' -> `0.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693001 none Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 39, 50, 20, 29, 15, 20, 11, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 20, 20, 20, 15, 15, 11, 11, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 165 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 mkdir: created directory `1' /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/1 /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Protomer 1 (index: 1000) grep: /scratch/xiaobo/167320/xcr-8058097.70/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: Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2) `ZINC001580693001.mol2' -> `1.mol2' `temp.mol2' -> `ZINC001580693001.mol2' antechamber (part of ambertools (downloadable for free!)) is not available on your computer obabel might write out a warning since atom types cannot be translated/interpreted correctly. The obabel warnings can be confidently disregarded. They don't affect the docking. 1 molecule converted running AMSOL7.1: SM5.42R (in water solvent) running AMSOL7.1: SM5.42R (in hexane solvent) `/scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/1/temp.mol2' -> `temp-working.mol2' `temp-working.mol2' -> `temp.mol2' `1.mol2' -> `1.mol2.original' `output.mol2' -> `1.mol2' warning *!*!* you are now running COVALENT omega script - expecting SiH3 i%d: 1 verbose debugging requested. {'rotateh': True, 'reseth': True, 'limitcoord': 1000000, 'verbose': True, 'timeit': False, 'db2gzfile': './output.1.db2in.mol2.db2.gz', 'clashfile': '/nfs/soft/dock/versions/dock37/DOCK-3.7-trunk/ligand/mol2db2/clashfile.txt', 'maxrecursiondepth': 1, 'mol2file': './output.1.db2in.mol2', 'hydrogenfile': None, 'atomtypefile': None, 'limitset': 2500000, 'limitconf': 200000, 'namefile': 'name.txt', 'covalent': True, 'colortablefile': None, 'tolerance': 0.001, 'solvfile': 'output.solv'} 18 is the cov attach 4 18 0 4 18 1 4 18 2 3 18 2 21 to be deleted 22 to be deleted 23 to be deleted natoms 56 natoms 55 natoms 54 natoms 53 names: ZINC001580693001 none Cc1ncc2n1C[C@@H](C(=O)N(C)CCNC(=O)[C@]([O-])([SiH3])C(C)(C)C)CC2 NO_LONG_NAME dock atom types: ['C.3', 'C.2', 'N.2', 'C.2', 'C.2', 'N.pl3', 'C.3', 'C.3', 'H', 'C.2', 'O.2', 'N.am', 'C.3', 'C.3', 'C.3', 'N.am', 'C.2', 'O.2', 'C.3', 'O.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'C.3', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H', 'H'] dock atom type numbers: [5, 1, 8, 1, 1, 8, 5, 5, 7, 1, 11, 8, 5, 5, 5, 8, 1, 11, 5, 12, 5, 5, 5, 5, 5, 5, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] dock color type numbers: [7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 6, 7, 7, 7, 7, 4, 9, 6, 8, 10, 11, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7, 7] 0 hydrogens need rotated 50 conformations 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, 50, 21, 29, 13, 21, 10, 2, 2, 1, 2, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50, 50, 50, 50, 50, 21, 21, 21, 13, 13, 10, 10, 2, 1, 1, 1, 1, 1, 1, 1, 1, 1, 50, 50, 50, 50] 50 rigid atoms, others: [48, 40, 41, 42, 43, 44, 45, 46, 47, 16, 18, 19, 20, 21, 22, 23] set([0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 17, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 49, 50, 51, 52]) total number of confs: 169 number of broken/clashed sets: 1 ./output.1.db2in.mol2.db2.gz file written out Cleaning up /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Finished preparing ZINC001580693001 Recording results /scratch/xiaobo/167320/xcr-8058097.70/working /scratch/xiaobo/167320/xcr-8058097.70 Appending to /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.* 1: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/1.* 0: /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001/0.* Removing working files in /scratch/xiaobo/167320/xcr-8058097.70/working/building/ZINC001580693001 /scratch/xiaobo/167320/xcr-8058097.70 Compressing combined databse files /scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.db2.gz ======================================================= WARNING: STORE_PROTOMERS not executable or a directory! All results left in place (/scratch/xiaobo/167320/xcr-8058097.70/finished) ======================================================= Finalizing... removed `/scratch/xiaobo/167320/xcr-8058097.70/working/3D/1001' removed directory: `/scratch/xiaobo/167320/xcr-8058097.70/working/3D' rmdir: removing directory, `/scratch/xiaobo/167320/xcr-8058097.70/working/building' rmdir: removing directory, `/scratch/xiaobo/167320/xcr-8058097.70/working' /mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/logs `/scratch/xiaobo/167320/xcr-8058097.70' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcr' `/scratch/xiaobo/167320/xcr-8058097.70/finished' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcr/finished' `/scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.db2.gz' -> `/mnt/nfs/exa/work/xiaobo/2020-3-19-main-protease/cis-trans-format/library-build-charge/jobs/xak/outputs/xcr/finished/xcr.db2.gz' removed `/scratch/xiaobo/167320/xcr-8058097.70/finished/xcr.db2.gz' removed directory: `/scratch/xiaobo/167320/xcr-8058097.70/finished' removed directory: `/scratch/xiaobo/167320/xcr-8058097.70'